Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008180.1 Hibiscus syriacus cultivar Beakdansim tig00110777_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: 2670214
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 14
Found at i:1966332 original size:20 final size:20
Alignment explanation
Indices: 1966123--1966337 Score: 168
Period size: 20 Copynumber: 10.7 Consensus size: 20
1966113 AGTTTCCAAT
* *
1966123 TTCGCAACACAAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
*
1966143 TTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
* *
1966163 -TCTGCAACACAAAAGTCAAA
1 TTC-GCAACGCGAAAGTCAAA
* *
1966183 TTCGCAATGCGAATTTGT-AAA
1 TTCGCAACGCGAA--AGTCAAA
**
1966204 -TCGCAAC-AAAGAAGTCAAA
1 TTCGCAACGCGA-AAGTCAAA
* * *
1966223 TTCACAACGCGATAGCCAAA
1 TTCGCAACGCGAAAGTCAAA
**
1966243 TTCGCAACGTAAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
* **
1966263 TTCGCAACACTGAATTTCAAA
1 TTCGCAACGC-GAAAGTCAAA
***
1966284 TTCGCAACATAAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
*
1966304 TTCGCAACGCGAAACTCAAA
1 TTCGCAACGCGAAAGTCAAA
1966324 TTCGCAACGCGAAA
1 TTCGCAACGCGAAA
1966338 TACAATATTA
Statistics
Matches: 149, Mismatches: 37, Indels: 18
0.73 0.18 0.09
Matches are distributed among these distances:
18 2 0.01
19 6 0.04
20 117 0.79
21 22 0.15
22 2 0.01
ACGTcount: A:0.43, C:0.24, G:0.14, T:0.19
Consensus pattern (20 bp):
TTCGCAACGCGAAAGTCAAA
Found at i:1966472 original size:22 final size:22
Alignment explanation
Indices: 1966447--1966497 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1966437 CTACGGTGAC
1966447 ATCCGTCCCCATCTCCAACGAA
1 ATCCGTCCCCATCTCCAACGAA
* **
1966469 ATCCATCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCAACGAA
1966491 ATCCGTC
1 ATCCGTC
1966498 TATCTTCATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.24, C:0.45, G:0.12, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCAACGAA
Found at i:1966916 original size:19 final size:21
Alignment explanation
Indices: 1966884--1966931 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
1966874 AAATCGCAAC
1966884 GCGATTTT-AGTTT-CACGTT
1 GCGATTTTCAGTTTCCACGTT
*
1966903 GCGATTTTCA-TTTCCGCGTT
1 GCGATTTTCAGTTTCCACGTT
*
1966923 GCAATTTTC
1 GCGATTTTC
1966932 TCGTTGCGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.46
Consensus pattern (21 bp):
GCGATTTTCAGTTTCCACGTT
Found at i:1969172 original size:21 final size:22
Alignment explanation
Indices: 1969124--1969179 Score: 87
Period size: 21 Copynumber: 2.6 Consensus size: 22
1969114 TGCGCCTCCT
1969124 ATCGTTCAAGAGGCCCCCTCTC
1 ATCGTTCAAGAGGCCCCCTCTC
* *
1969146 ACCGTTCAAGAGG-CCCCTGTC
1 ATCGTTCAAGAGGCCCCCTCTC
1969167 ATCGTTCAAGAGG
1 ATCGTTCAAGAGG
1969180 TCCCACCTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
21 19 0.61
22 12 0.39
ACGTcount: A:0.21, C:0.34, G:0.23, T:0.21
Consensus pattern (22 bp):
ATCGTTCAAGAGGCCCCCTCTC
Found at i:1970666 original size:65 final size:65
Alignment explanation
Indices: 1970529--1970704 Score: 255
Period size: 66 Copynumber: 2.6 Consensus size: 65
1970519 GGGGTACACT
*
1970529 TTTTTTTGCTTGTTTAATTGAATTTTACATTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAG
1 TTTTTTTGCTTGTTTAATTG-A-TTT---GTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAG
1970594 AATTA
61 AATTA
* *
1970599 -TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATT
1 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATT
1970663 A
65 A
*
1970664 TTTTTTTTCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1970705 GTTTTAAATT
Statistics
Matches: 100, Mismatches: 4, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
64 19 0.19
65 19 0.19
66 39 0.39
67 3 0.03
68 1 0.01
69 19 0.19
ACGTcount: A:0.28, C:0.02, G:0.16, T:0.53
Consensus pattern (65 bp):
TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA
Found at i:1970813 original size:20 final size:20
Alignment explanation
Indices: 1970758--1970806 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1970748 GTTGAAGGTA
1970758 CAAATTCGCAACGCGAAAAT
1 CAAATTCGCAACGCGAAAAT
*
1970778 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAAT
1970798 CAAATTCGC
1 CAAATTCGC
1970807 GTTGCGATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.41, C:0.27, G:0.16, T:0.16
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAAT
Found at i:1971144 original size:12 final size:12
Alignment explanation
Indices: 1971129--1971169 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
1971119 AAGCCGGTTG
1971129 TGATTGAGATTT
1 TGATTGAGATTT
**
1971141 TGATTTTGATTT
1 TGATTGAGATTT
*
1971153 TGATTGCGATTT
1 TGATTGAGATTT
1971165 TGATT
1 TGATT
1971170 TCCTTTTGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.20, C:0.02, G:0.22, T:0.56
Consensus pattern (12 bp):
TGATTGAGATTT
Found at i:1971145 original size:6 final size:6
Alignment explanation
Indices: 1971136--1971170 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1971126 TTGTGATTGA
**
1971136 GATTTT GATTTT GATTTT GATTGC GATTTT GATTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTT
1971171 CCTTTTGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.17, C:0.03, G:0.20, T:0.60
Consensus pattern (6 bp):
GATTTT
Found at i:1973334 original size:24 final size:24
Alignment explanation
Indices: 1973297--1973350 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1973287 CTGAAACATC
*
1973297 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
* * *
1973321 ATCAAAGTCTGAGTATTAACTAAG
1 ATCAAAATCCGAGTATTAACCAAG
1973345 ATCAAA
1 ATCAAA
1973351 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:1973497 original size:12 final size:12
Alignment explanation
Indices: 1973476--1973509 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1973466 TGGTGTGGGT
*
1973476 TTTGAGATTGTG
1 TTTGATATTGTG
1973488 TTTGATATTGTG
1 TTTGATATTGTG
*
1973500 TTTGGTATTG
1 TTTGATATTG
1973510 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:1974342 original size:20 final size:19
Alignment explanation
Indices: 1974317--1974365 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
1974307 TTAAATTCGT
1974317 GTTGCGAATTCAAAAATCTA
1 GTTGCGAATTCAAAAATC-A
** *
1974337 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTCAAAAATCA
1974356 GTTGCGAATT
1 GTTGCGAATT
1974366 TGAAATTCAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (19 bp):
GTTGCGAATTCAAAAATCA
Found at i:1974358 original size:19 final size:19
Alignment explanation
Indices: 1974317--1974392 Score: 98
Period size: 19 Copynumber: 3.9 Consensus size: 19
1974307 TTAAATTCGT
** *
1974317 GTTGCGAATTCAAAAATCTA
1 GTTGCGAATTTGAAATTC-A
1974337 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
1974356 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
* *
1974375 GTTACAAATTTGAAATTC
1 GTTGCGAATTTGAAATTC
1974393 CGCGTTGTGA
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 36 0.71
20 15 0.29
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:1974425 original size:20 final size:20
Alignment explanation
Indices: 1974396--1974467 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 20
1974386 GAAATTCCGC
*
1974396 GTTGTGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* * * *
1974416 GTTGCAAATTTGACTATCGC
1 GTTGCGAATTTGACTTTTGT
*
1974436 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTTTGT
1974456 GTTGCGAATTTG
1 GTTGCGAATTTG
1974468 GAAAATCGCA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.18, C:0.12, G:0.25, T:0.44
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:1976344 original size:20 final size:20
Alignment explanation
Indices: 1976316--1976406 Score: 150
Period size: 20 Copynumber: 4.7 Consensus size: 20
1976306 ATTACACCAA
* *
1976316 TATCACTTAAGGTGTCTTAT
1 TATCCCTTAAGGTCTCTTAT
1976336 TATCCCTTAAGGTCTCTTAT
1 TATCCCTTAAGGTCTCTTAT
1976356 TATCCCTTAAGG--TCTTAT
1 TATCCCTTAAGGTCTCTTAT
1976374 TATCCCTTAAGGTCTCTTAT
1 TATCCCTTAAGGTCTCTTAT
1976394 TATCCCTTAAGGT
1 TATCCCTTAAGGT
1976407 TCTGTGATTG
Statistics
Matches: 67, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
18 18 0.27
20 49 0.73
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (20 bp):
TATCCCTTAAGGTCTCTTAT
Found at i:1976374 original size:38 final size:38
Alignment explanation
Indices: 1976329--1976406 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
1976319 CACTTAAGGT
1976329 GTCTTATTATCCCTTAAGGTCTCTTATTATCCCTTAAG
1 GTCTTATTATCCCTTAAGGTCTCTTATTATCCCTTAAG
1976367 GTCTTATTATCCCTTAAGGTCTCTTATTATCCCTTAAG
1 GTCTTATTATCCCTTAAGGTCTCTTATTATCCCTTAAG
1976405 GT
1 GT
1976407 TCTGTGATTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.45
Consensus pattern (38 bp):
GTCTTATTATCCCTTAAGGTCTCTTATTATCCCTTAAG
Found at i:1978352 original size:2 final size:2
Alignment explanation
Indices: 1978345--1978388 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1978335 CAGCATTTTG
1978345 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
1978387 AT
1 AT
1978389 GTCAAGTCTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1978825 original size:34 final size:34
Alignment explanation
Indices: 1978782--1978850 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
1978772 GGAGCTTTCT
1978782 TGTTGAGGGGAATGTTATCTGGTTCAAGACCAAC
1 TGTTGAGGGGAATGTTATCTGGTTCAAGACCAAC
1978816 TGTTGAGGGGAATGTTATCTGGTTCAAGACCAAC
1 TGTTGAGGGGAATGTTATCTGGTTCAAGACCAAC
1978850 T
1 T
1978851 TCTTTTTCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.30
Consensus pattern (34 bp):
TGTTGAGGGGAATGTTATCTGGTTCAAGACCAAC
Found at i:1983677 original size:2 final size:2
Alignment explanation
Indices: 1983670--1983728 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
1983660 TGAATTATGA
1983670 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
1983712 AT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1983729 TCAAAAATTG
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1993462 original size:12 final size:12
Alignment explanation
Indices: 1993445--1993480 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
1993435 TTTAAGGCTT
1993445 TCTCTTTGATTC
1 TCTCTTTGATTC
1993457 TCTCTTTGATTC
1 TCTCTTTGATTC
1993469 TCTC-TTGATTC
1 TCTCTTTGATTC
1993480 T
1 T
1993481 TGTTTCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.08, C:0.25, G:0.08, T:0.58
Consensus pattern (12 bp):
TCTCTTTGATTC
Found at i:1993888 original size:55 final size:54
Alignment explanation
Indices: 1993779--1993900 Score: 147
Period size: 55 Copynumber: 2.2 Consensus size: 54
1993769 TGCATCTGTT
** * * * *
1993779 GTGTATCGGTATACAAAATGCATTTGATGTTGGGGTGTATTAGTACATCAAAGA
1 GTGTATCGGTACCCAAAATACATTCGATATTGGGGTGTATGAGTACATCAAAGA
* *
1993833 GTGTATCGGTACCCAAATTACATTCGATATTGGGGGTGTATCGA-TACATCCAAGA
1 GTGTATCGGTACCCAAAATACATTCGATATT-GGGGTGTAT-GAGTACATCAAAGA
1993888 GTGTATCGGTACC
1 GTGTATCGGTACC
1993901 TCCCTTTGTA
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
54 25 0.43
55 32 0.55
56 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (54 bp):
GTGTATCGGTACCCAAAATACATTCGATATTGGGGTGTATGAGTACATCAAAGA
Found at i:1994228 original size:12 final size:13
Alignment explanation
Indices: 1994201--1994233 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1994191 TAAGATTTTC
1994201 TTTGAAAACTATT
1 TTTGAAAACTATT
*
1994214 TTTGAAATC-ATT
1 TTTGAAAACTATT
1994226 TTTGAAAA
1 TTTGAAAA
1994234 TTACTCCACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.45
Consensus pattern (13 bp):
TTTGAAAACTATT
Found at i:1995999 original size:12 final size:13
Alignment explanation
Indices: 1995982--1996014 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1995972 ATGGGAAAAA
*
1995982 TTTGAAAACTAT-
1 TTTGAAAACAATG
1995994 TTTGAAAACAATG
1 TTTGAAAACAATG
1996007 TTTGAAAA
1 TTTGAAAA
1996015 ATCATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (13 bp):
TTTGAAAACAATG
Found at i:1996543 original size:21 final size:22
Alignment explanation
Indices: 1996485--1996567 Score: 64
Period size: 21 Copynumber: 3.8 Consensus size: 22
1996475 AAAACCGGAC
*
1996485 GAGTGTATCGATACAC-ATTCAA
1 GAGTGTATCGATACACTAGTC-A
* * *
1996507 GGAATGCATCGGTACACTA-TCA
1 -GAGTGTATCGATACACTAGTCA
* *
1996529 TAGTGTATCGATACA-TAGTGA
1 GAGTGTATCGATACACTAGTCA
*
1996550 GGGTGTATCGATACACTA
1 GAGTGTATCGATACACTA
1996568 CGCACAAAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
20 2 0.04
21 26 0.55
22 3 0.06
23 15 0.32
24 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.28
Consensus pattern (22 bp):
GAGTGTATCGATACACTAGTCA
Found at i:2000933 original size:23 final size:23
Alignment explanation
Indices: 2000915--2000975 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
2000905 CTCATATAAA
*
2000915 TGCACCGAAGTGCCACATACAAT
1 TGCACCGTAGTGCCACATACAAT
* * *
2000938 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATACAAT
2000961 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
2000976 TATAATAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.26, C:0.30, G:0.25, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATACAAT
Found at i:2001162 original size:103 final size:103
Alignment explanation
Indices: 2000991--2001208 Score: 436
Period size: 103 Copynumber: 2.1 Consensus size: 103
2000981 TAATGTCCAT
2000991 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
2001056 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
2001094 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
2001159 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
2001197 AAGGACCACATA
1 AAGGACCACATA
2001209 GACCCTCGAC
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 115 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:2002236 original size:2 final size:2
Alignment explanation
Indices: 2002229--2002285 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
2002219 ATATTTCATT
2002229 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2002271 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
2002286 CAAAGATCTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2005840 original size:54 final size:55
Alignment explanation
Indices: 2005762--2005883 Score: 174
Period size: 55 Copynumber: 2.2 Consensus size: 55
2005752 TACATCTGTT
* * *
2005762 GTGTATCGGTACACAAAATGCATTCGATGTT-GGGGTGTATCGGTACATCAAAGA
1 GTGTATCGGTACCCAAAATACATTCGATGTTGGGGGTGTATCGATACATCAAAGA
* * *
2005816 GTGTATCGGTACCCAAATTACATTCGATGTTGGGGGTGTATTGATACATCCAAGA
1 GTGTATCGGTACCCAAAATACATTCGATGTTGGGGGTGTATCGATACATCAAAGA
*
2005871 GTGTATCAGTACC
1 GTGTATCGGTACC
2005884 ACCCTTTGTA
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
54 28 0.47
55 32 0.53
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (55 bp):
GTGTATCGGTACCCAAAATACATTCGATGTTGGGGGTGTATCGATACATCAAAGA
Found at i:2007898 original size:18 final size:18
Alignment explanation
Indices: 2007875--2007919 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
2007865 TAACAGAATG
*
2007875 TAAGATTATCAGCGAGAA
1 TAAGATTACCAGCGAGAA
* *
2007893 TAAGATTACCGGCGGGAA
1 TAAGATTACCAGCGAGAA
2007911 TAAGATTAC
1 TAAGATTAC
2007920 TGAGAATGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.22
Consensus pattern (18 bp):
TAAGATTACCAGCGAGAA
Found at i:2009959 original size:20 final size:20
Alignment explanation
Indices: 2009934--2010103 Score: 241
Period size: 20 Copynumber: 8.4 Consensus size: 20
2009924 TTTTCCTAAT
2009934 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
2009954 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
2009975 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
2009995 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
2010015 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
2010035 TCGCAATGCGATTATGTAAA
1 TCGCAATGCGAATACGTAAA
* *
2010055 TCGTAATGCGAATACATAAA
1 TCGCAATGCGAATACGTAAA
*
2010075 TCGCAATGCGAATACATAAA
1 TCGCAATGCGAATACGTAAA
2010095 TCGCAATGC
1 TCGCAATGC
2010104 AAATCTGACT
Statistics
Matches: 132, Mismatches: 17, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
20 117 0.89
21 15 0.11
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:2010118 original size:40 final size:40
Alignment explanation
Indices: 2009934--2010125 Score: 196
Period size: 40 Copynumber: 4.8 Consensus size: 40
2009924 TTTTCCTAAT
* ** *
2009934 TCGCAATGCGAATAC-GTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATACTG-AAATCGCAATGCGAA-TACGTAAA
*
2009975 TCGCAATGCGATTAC-GTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACTG-AAATCGCAATGCGAATACGTAAA
* *
2010015 TCGCAATGCGAATAC-GTAAATCGCAATGCGATTATGTAAA
1 TCGCAATGCGAATACTG-AAATCGCAATGCGAATACGTAAA
* *
2010055 TCGTAATGCGAATACAT-AAATCGCAATGCGAATACATAAA
1 TCGCAATGCGAATAC-TGAAATCGCAATGCGAATACGTAAA
* *
2010095 TCGCAATGCAAAT-CTGACTATCGCAATGCGA
1 TCGCAATGCGAATACTGA-AATCGCAATGCGA
2010126 TTTACATAGC
Statistics
Matches: 132, Mismatches: 15, Indels: 9
0.85 0.10 0.06
Matches are distributed among these distances:
38 1 0.01
39 2 0.02
40 99 0.75
41 30 0.23
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (40 bp):
TCGCAATGCGAATACTGAAATCGCAATGCGAATACGTAAA
Found at i:2010123 original size:60 final size:58
Alignment explanation
Indices: 2009934--2010125 Score: 192
Period size: 60 Copynumber: 3.2 Consensus size: 58
2009924 TTTTCCTAAT
* ** *
2009934 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGA-AAATCGCAATGCGATT-ACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAA--TACATAAATCGCAATGCAATTGAC-T--A
* * *
2009995 TCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAATCGCAATGCGATTATGTA-AA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATACATAAATCGCAATGC-AAT-TG-ACTA
* *
2010055 TCGTAATGCGAATACATAAATCGCAATGCGAATACATAAATCGCAATGCAAATCTGACTA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATACATAAATCGCAATGC-AAT-TGACTA
2010115 TCGCAATGCGA
1 TCGCAATGCGA
2010126 TTTACATAGC
Statistics
Matches: 110, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
59 2 0.02
60 74 0.67
61 32 0.29
62 1 0.01
64 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (58 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGAATACATAAATCGCAATGCAATTGACTA
Found at i:2010738 original size:33 final size:34
Alignment explanation
Indices: 2010690--2010762 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 34
2010680 ACTATCGCAA
** *
2010690 TGCGATTCTGTCGTTGCGATTTTC-ATTTCGCGT
1 TGCGATTCTGTCGTTGCGATAGTCAAATTCGCGT
2010723 TGCGATTCT-TGCGTTGCGATAGTCAAATTCGCGT
1 TGCGATTCTGT-CGTTGCGATAGTCAAATTCGCGT
2010757 TGCGAT
1 TGCGAT
2010763 AGTCATTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 20 0.57
34 14 0.40
ACGTcount: A:0.14, C:0.21, G:0.26, T:0.40
Consensus pattern (34 bp):
TGCGATTCTGTCGTTGCGATAGTCAAATTCGCGT
Found at i:2010758 original size:20 final size:20
Alignment explanation
Indices: 2010733--2010782 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
2010723 TGCGATTCTT
2010733 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
**
2010753 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCAAATTC
*
2010773 GTGTTGCGAT
1 GCGTTGCGAT
2010783 TTTCATTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAATTC
Found at i:2010788 original size:20 final size:20
Alignment explanation
Indices: 2010750--2010804 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
2010740 GATAGTCAAA
* **
2010750 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
2010770 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
*
2010790 TTCGTGTTGCAATTT
1 TTCGTGTTGCGATTT
2010805 AAAGTTTCAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.13, C:0.16, G:0.22, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:2010812 original size:20 final size:20
Alignment explanation
Indices: 2010769--2010812 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
2010759 CGATAGTCAT
* ** *
2010769 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCAATTTAAAG
2010789 TTTCGTGTTGCAATTTAAAG
1 TTTCGTGTTGCAATTTAAAG
2010809 TTTC
1 TTTC
2010813 AGAAACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.14, G:0.18, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCAATTTAAAG
Found at i:2012691 original size:20 final size:20
Alignment explanation
Indices: 2012666--2012795 Score: 215
Period size: 20 Copynumber: 6.5 Consensus size: 20
2012656 AGAATAGTTT
**
2012666 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAATTTG
**
2012686 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAATTTG
2012706 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAATTTG
2012726 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAATTTG
2012746 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAATTTG
*
2012766 ACTATCTCAATGCGAATTTG
1 ACTATCGCAATGCGAATTTG
2012786 ACTATCGCAA
1 ACTATCGCAA
2012796 CGAAAGAATC
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 106 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (20 bp):
ACTATCGCAATGCGAATTTG
Found at i:2012879 original size:20 final size:20
Alignment explanation
Indices: 2012840--2012888 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
2012830 GCGATTCTCT
**
2012840 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
2012860 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
2012880 TGTTGCGAT
1 CGTTGCGAT
2012889 TTTGTTGTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:2012900 original size:34 final size:34
Alignment explanation
Indices: 2012860--2012955 Score: 104
Period size: 33 Copynumber: 2.9 Consensus size: 34
2012850 GTCAAATTCG
* * *
2012860 CATTGCGATAGTCATTTTCGTGTTGCGATTTTGT
1 CATTGCGATAGTCATTTTCGCGTTGCGATTCTCT
** ** *
2012894 TGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CATTGCGATAGTCATTTTCGCGTTGCGATTCTCT
*
2012927 CATTACGATAGTCATTTTCGCGTTGCGAT
1 CATTGCGATAGTCATTTTCGCGTTGCGAT
2012956 AGTCATTTTC
Statistics
Matches: 47, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
33 24 0.51
34 23 0.49
ACGTcount: A:0.16, C:0.19, G:0.21, T:0.45
Consensus pattern (34 bp):
CATTGCGATAGTCATTTTCGCGTTGCGATTCTCT
Found at i:2012957 original size:20 final size:20
Alignment explanation
Indices: 2012932--2013015 Score: 132
Period size: 20 Copynumber: 4.2 Consensus size: 20
2012922 TCTCTCATTA
2012932 CGATAGTCATTTTCGCGTTG
1 CGATAGTCATTTTCGCGTTG
*
2012952 CGATAGTCATTTTCGCGTTA
1 CGATAGTCATTTTCGCGTTG
*
2012972 CGATAGTCATTTTCACGTTG
1 CGATAGTCATTTTCGCGTTG
* *
2012992 TGATAGCCATTTTCGCGTTG
1 CGATAGTCATTTTCGCGTTG
2013012 CGAT
1 CGAT
2013016 TTTAAGTTTC
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (20 bp):
CGATAGTCATTTTCGCGTTG
Found at i:2013026 original size:40 final size:40
Alignment explanation
Indices: 2012929--2013026 Score: 106
Period size: 40 Copynumber: 2.5 Consensus size: 40
2012919 GATTCTCTCA
* * * *
2012929 TTACGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCG
1 TTACGATAGTAAGTTTCACGTTGCGATAGCCATTTTCGCG
* * *
2012969 TTACGATAGTCATTTTCACGTTGTGATAGCCATTTTCGCG
1 TTACGATAGTAAGTTTCACGTTGCGATAGCCATTTTCGCG
* **
2013009 TTGCGATTTTAAGTTTCA
1 TTACGATAGTAAGTTTCA
2013027 GATTCTATTC
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.19, C:0.18, G:0.20, T:0.42
Consensus pattern (40 bp):
TTACGATAGTAAGTTTCACGTTGCGATAGCCATTTTCGCG
Found at i:2015178 original size:34 final size:33
Alignment explanation
Indices: 2015096--2015180 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 33
2015086 TCGCAACGCG
** * *
2015096 GAAATGACTATCGCGACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCACAATGC
* *
2015129 GAAATGAAAACCGCAACGAGTGAATCACAATGC
1 GAAATGAAAATCGCAACGAGAGAATCACAATGC
2015162 GAAAATGAAAATCGCAACG
1 G-AAATGAAAATCGCAACG
2015181 CGAAACTAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 28 0.64
34 16 0.36
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.13
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCACAATGC
Found at i:2015258 original size:33 final size:34
Alignment explanation
Indices: 2015195--2015270 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 34
2015185 ACTAATTTCG
*
2015195 CGTTGCGATTTTCATTTTCGAATTGTGATTCACT
1 CGTTGCGATTTTCATTTTCGAATTGCGATTCACT
* *
2015229 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGAATTGCGATTCACT
2015262 CGTTGCGAT
1 CGTTGCGAT
2015271 AGTCAATTCC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 25 0.64
34 14 0.36
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.45
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGAATTGCGATTCACT
Found at i:2015326 original size:20 final size:21
Alignment explanation
Indices: 2015262--2015327 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 21
2015252 GCGATTCTCT
*
2015262 CGTTGCGATAGTCA-ATTCCA
1 CGTTGCGATAGTCATATTCCG
*
2015282 CATTGC-ATTAGTCAT-TTCCG
1 CGTTGCGA-TAGTCATATTCCG
*
2015302 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCATATTCCG
2015322 CGTTGC
1 CGTTGC
2015328 TATTTCTGCG
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
19 1 0.03
20 33 0.89
21 3 0.08
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (21 bp):
CGTTGCGATAGTCATATTCCG
Found at i:2017771 original size:13 final size:13
Alignment explanation
Indices: 2017753--2017806 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 13
2017743 GATCGGTCAC
2017753 GACCCGACCCGTT
1 GACCCGACCCGTT
2017766 GACCCGACCCGACCGTT
1 GACCCGA--C--CCGTT
* *
2017783 GACCTGACCAGTT
1 GACCCGACCCGTT
2017796 GACCCGACCCG
1 GACCCGACCCG
2017807 ACCGTTGACC
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
13 20 0.61
15 2 0.06
17 11 0.33
ACGTcount: A:0.19, C:0.44, G:0.24, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:2017798 original size:30 final size:30
Alignment explanation
Indices: 2017753--2017816 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
2017743 GATCGGTCAC
*
2017753 GACCCGACCCGTTGACCCGACCCGACCGTT
1 GACCCGACCAGTTGACCCGACCCGACCGTT
*
2017783 GACCTGACCAGTTGACCCGACCCGACCGTT
1 GACCCGACCAGTTGACCCGACCCGACCGTT
2017813 GACC
1 GACC
2017817 GGTGCTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.19, C:0.44, G:0.23, T:0.14
Consensus pattern (30 bp):
GACCCGACCAGTTGACCCGACCCGACCGTT
Found at i:2017859 original size:29 final size:29
Alignment explanation
Indices: 2017817--2017897 Score: 110
Period size: 29 Copynumber: 2.8 Consensus size: 29
2017807 ACCGTTGACC
* **
2017817 GGTGCTATTTTGGTAAATAATTTGGTTTT
1 GGTGCTATTATGGTAAATAATTCAGTTTT
2017846 GGTGCTATTATGGTAAATAATTCAGTTTT
1 GGTGCTATTATGGTAAATAATTCAGTTTT
*
2017875 GGTGCTATTCA-GGTAATTAATTC
1 GGTGCTATT-ATGGTAAATAATTC
2017898 GAAATGGGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
29 46 0.98
30 1 0.02
ACGTcount: A:0.25, C:0.07, G:0.22, T:0.46
Consensus pattern (29 bp):
GGTGCTATTATGGTAAATAATTCAGTTTT
Found at i:2017942 original size:29 final size:29
Alignment explanation
Indices: 2017875--2017942 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
2017865 ATTCAGTTTT
* * *
2017875 GGTGCTATTCAGGTAATTAATTCGAAATG
1 GGTGCTATTTAGGTAATTAATTCAAAAAG
* * *
2017904 GGTGCTATTTTGGTAATTATTTTAAAAAG
1 GGTGCTATTTAGGTAATTAATTCAAAAAG
2017933 GGTGCTATTT
1 GGTGCTATTT
2017943 GTGTAAAATG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41
Consensus pattern (29 bp):
GGTGCTATTTAGGTAATTAATTCAAAAAG
Found at i:2025333 original size:29 final size:29
Alignment explanation
Indices: 2025291--2025370 Score: 151
Period size: 29 Copynumber: 2.8 Consensus size: 29
2025281 ACCGTTGACC
*
2025291 GGTGCTATTTTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTCAGTTTT
2025320 GGTGCTATTCTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTCAGTTTT
2025349 GGTGCTATTCTGGTAAATAATT
1 GGTGCTATTCTGGTAAATAATT
2025371 TGAAATGGGT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.25, C:0.09, G:0.21, T:0.45
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCAGTTTT
Found at i:2025381 original size:29 final size:29
Alignment explanation
Indices: 2025291--2025423 Score: 106
Period size: 29 Copynumber: 4.6 Consensus size: 29
2025281 ACCGTTGACC
* * *** *
2025291 GGTGCTATTTTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTTAAAATG
* *** *
2025320 GGTGCTATTCTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTTAAAATG
*
2025349 GGTGCTATTCTGGTAAATAATTTGAAATG
1 GGTGCTATTCTGGTAAATAATTTAAAATG
* * * *
2025378 GGTGCTATTTTGGTAATTATTTTAAAAAG
1 GGTGCTATTCTGGTAAATAATTTAAAATG
2025407 GGTGCTATT-TGTGTAAA
1 GGTGCTATTCTG-GTAAA
2025424 ATGTTCAATA
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
28 2 0.02
29 88 0.98
ACGTcount: A:0.27, C:0.07, G:0.23, T:0.44
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTTAAAATG
Found at i:2027836 original size:24 final size:24
Alignment explanation
Indices: 2027802--2027855 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2027792 CTGAAAAATC
2027802 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2027826 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2027850 ATCAAA
1 ATCAAA
2027856 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2027869 original size:24 final size:24
Alignment explanation
Indices: 2027802--2027869 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
2027792 CTGAAAAATC
* * *
2027802 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
2027826 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
2027850 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
2027870 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:2028757 original size:12 final size:12
Alignment explanation
Indices: 2028742--2028766 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2028732 CAGATTCGTA
2028742 TTGCGATTTACG
1 TTGCGATTTACG
2028754 TTGCGATTTACG
1 TTGCGATTTACG
2028766 T
1 T
2028767 AATCGCATTG
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:0.16, C:0.16, G:0.24, T:0.44
Consensus pattern (12 bp):
TTGCGATTTACG
Found at i:2028777 original size:32 final size:32
Alignment explanation
Indices: 2028720--2028782 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
2028710 GTCAGAATCT
* * *
2028720 CGTTGCGATTTACAGATTCGTATTGCGATTTA
1 CGTTGCGATTTACAGAATCGCATTGCAATTTA
2028752 CGTTGCGATTTAC-GTAATCGCATTGCAATTT
1 CGTTGCGATTTACAG-AATCGCATTGCAATTT
2028783 TCCAAATTCG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 1 0.04
32 26 0.96
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.40
Consensus pattern (32 bp):
CGTTGCGATTTACAGAATCGCATTGCAATTTA
Found at i:2028782 original size:20 final size:20
Alignment explanation
Indices: 2028754--2028823 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
2028744 GCGATTTACG
*
2028754 TTGCGATTTACGTAATCGCA
1 TTGCAATTTACGTAATCGCA
* ** *
2028774 TTGCAATTTTCCAAATTCGCG
1 TTGCAATTTACGTAA-TCGCA
* *
2028795 TTGCGATTTACGTATTCGCA
1 TTGCAATTTACGTAATCGCA
2028815 TTGCGAATT
1 TTGC-AATT
2028824 AGGAAAATCG
Statistics
Matches: 36, Mismatches: 12, Indels: 3
0.71 0.24 0.06
Matches are distributed among these distances:
20 19 0.53
21 17 0.47
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.39
Consensus pattern (20 bp):
TTGCAATTTACGTAATCGCA
Found at i:2037805 original size:21 final size:21
Alignment explanation
Indices: 2037762--2037805 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2037752 AATATAAATT
*
2037762 GTGTATCGATGCACTGCTACA
1 GTGTATCGATGCACTACTACA
*
2037783 GTGTATCGATGCACTACTGCA
1 GTGTATCGATGCACTACTACA
2037804 GT
1 GT
2037806 AACTTCGGAA
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:0.23, G:0.25, T:0.30
Consensus pattern (21 bp):
GTGTATCGATGCACTACTACA
Found at i:2044003 original size:15 final size:16
Alignment explanation
Indices: 2043985--2044016 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2043975 CCCTTGCAAA
2043985 AATTAAAATGA-AAAT
1 AATTAAAATGAGAAAT
2044000 AATTAAAATGAGAAAT
1 AATTAAAATGAGAAAT
2044016 A
1 A
2044017 TGAAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (16 bp):
AATTAAAATGAGAAAT
Found at i:2049911 original size:31 final size:31
Alignment explanation
Indices: 2049873--2049945 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
2049863 GAGTCGATGG
*
2049873 TTACCTATGTCTTTCGAGACATATGAATA-T
1 TTACCTATGTCTTTCAAGACATATGAATAGT
*
2049903 ATTACCTATGTCTTTCAAGACATATGGATAGT
1 -TTACCTATGTCTTTCAAGACATATGAATAGT
2049935 TTACCTATGTC
1 TTACCTATGTC
2049946 CTTAGGGATA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
31 38 0.97
32 1 0.03
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.40
Consensus pattern (31 bp):
TTACCTATGTCTTTCAAGACATATGAATAGT
Found at i:2049989 original size:30 final size:30
Alignment explanation
Indices: 2049903--2049991 Score: 81
Period size: 30 Copynumber: 2.9 Consensus size: 30
2049893 ATATGAATAT
* * *
2049903 ATTACCTATGTCTTTCAAG-ACATATGGATA
1 ATTACCTATGTCCTT-AGGAACATATGGACA
* * *
2049933 GTTTACCTATGTCCTTAGGGATATATGGACA
1 -ATTACCTATGTCCTTAGGAACATATGGACA
* *
2049964 ATTACCTATGTTCTTCGGAACATATGGA
1 ATTACCTATGTCCTTAGGAACATATGGA
2049992 TAGGGGTCCT
Statistics
Matches: 47, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
30 25 0.53
31 22 0.47
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (30 bp):
ATTACCTATGTCCTTAGGAACATATGGACA
Found at i:2050320 original size:18 final size:19
Alignment explanation
Indices: 2050297--2050332 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2050287 AAATGACTTA
*
2050297 TATTATGATATA-AGAATC
1 TATTATGAGATATAGAATC
2050315 TATTATGAGATATAGAAT
1 TATTATGAGATATAGAAT
2050333 ATGAATGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.44, C:0.03, G:0.14, T:0.39
Consensus pattern (19 bp):
TATTATGAGATATAGAATC
Found at i:2052392 original size:9 final size:9
Alignment explanation
Indices: 2052375--2052419 Score: 63
Period size: 9 Copynumber: 5.0 Consensus size: 9
2052365 AAGACATATG
2052375 AATGATAAT
1 AATGATAAT
*
2052384 AATGTTAAT
1 AATGATAAT
*
2052393 AATGATAAG
1 AATGATAAT
*
2052402 AATAATAAT
1 AATGATAAT
2052411 AATGATAAT
1 AATGATAAT
2052420 GATAATGAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (9 bp):
AATGATAAT
Found at i:2052398 original size:18 final size:18
Alignment explanation
Indices: 2052375--2052425 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
2052365 AAGACATATG
**
2052375 AATGATAATAATGTTAAT
1 AATGATAATAATAATAAT
*
2052393 AATGATAAGAATAATAAT
1 AATGATAATAATAATAAT
*
2052411 AATGATAATGATAAT
1 AATGATAATAATAAT
2052426 GAAATGATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (18 bp):
AATGATAATAATAATAAT
Found at i:2052400 original size:6 final size:6
Alignment explanation
Indices: 2052391--2052433 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
2052381 AATAATGTTA
*
2052391 ATAATG ATAA-G AATAATA ATAATG ATAATG ATAATG A-AATG AT
1 ATAATG ATAATG -ATAATG ATAATG ATAATG ATAATG ATAATG AT
2052434 TTGTATATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 6 0.19
6 26 0.81
ACGTcount: A:0.56, C:0.00, G:0.14, T:0.30
Consensus pattern (6 bp):
ATAATG
Found at i:2059128 original size:54 final size:54
Alignment explanation
Indices: 2059036--2059211 Score: 237
Period size: 54 Copynumber: 3.3 Consensus size: 54
2059026 ACCGTATCGA
* *
2059036 CACTATGTGTGCAACCTAAGTAATTCATAATGAGTTTGTGAATTACTGTATTGG
1 CACTATGTGTGCAACCTACGCAATTCATAATGAGTTTGTGAATTACTGTATTGG
* * * *
2059090 CACTCTGTGTGCAACAC-ACGCAATTCATAAAGAATTTGTGAATTACTGTATTAG
1 CACTATGTGTGCAAC-CTACGCAATTCATAATGAGTTTGTGAATTACTGTATTGG
* * * * *
2059144 CACTATGCGTGCAACCTACGTAATTCACAATGAGTTTGTGAATTACCGTATCGG
1 CACTATGTGTGCAACCTACGCAATTCATAATGAGTTTGTGAATTACTGTATTGG
2059198 CACTATGTGTGCAA
1 CACTATGTGTGCAA
2059212 AACCAAGAAA
Statistics
Matches: 104, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
53 1 0.01
54 102 0.98
55 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Consensus pattern (54 bp):
CACTATGTGTGCAACCTACGCAATTCATAATGAGTTTGTGAATTACTGTATTGG
Found at i:2070634 original size:2 final size:2
Alignment explanation
Indices: 2070627--2070654 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2070617 CAACAAAAAT
2070627 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2070655 ATTATCAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2073245 original size:21 final size:21
Alignment explanation
Indices: 2073221--2073265 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2073211 CATATCAAGC
*
2073221 ATAAATGTTCTTGATCATTTT
1 ATAAATGTTCTTAATCATTTT
*
2073242 ATAAATGTTTTTAATCATTTT
1 ATAAATGTTCTTAATCATTTT
2073263 ATA
1 ATA
2073266 TATGATACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (21 bp):
ATAAATGTTCTTAATCATTTT
Found at i:2073329 original size:48 final size:48
Alignment explanation
Indices: 2073262--2073364 Score: 188
Period size: 48 Copynumber: 2.1 Consensus size: 48
2073252 TTAATCATTT
*
2073262 TATATATGATACATATCAAGAATAAATGTTCTTAACCAAATATATATA
1 TATATATGATACATATCAAGAATAAATGTACTTAACCAAATATATATA
*
2073310 TATATATGATACATATCAAGAATAAATGTACTTAATCAAATATATATA
1 TATATATGATACATATCAAGAATAAATGTACTTAACCAAATATATATA
2073358 TATATAT
1 TATATAT
2073365 ATATGATATA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.37
Consensus pattern (48 bp):
TATATATGATACATATCAAGAATAAATGTACTTAACCAAATATATATA
Found at i:2074503 original size:31 final size:31
Alignment explanation
Indices: 2074480--2074620 Score: 255
Period size: 31 Copynumber: 4.5 Consensus size: 31
2074470 CATAGATTCT
* *
2074480 GAAGAACCTAGGTAATCAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
2074511 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
2074542 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
2074573 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
*
2074604 AAAGAACATAGGTAAAC
1 GAAGAACATAGGTAAAC
2074621 CCTCAACCCT
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 107 1.00
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.19
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAGTCCATATGTCCC
Found at i:2075007 original size:12 final size:13
Alignment explanation
Indices: 2074990--2075018 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2074980 CATATTTTCA
2074990 TATAATATA-TCT
1 TATAATATATTCT
2075002 TATAATATATTCT
1 TATAATATATTCT
2075015 TATA
1 TATA
2075019 TCATCATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (13 bp):
TATAATATATTCT
Found at i:2075566 original size:21 final size:21
Alignment explanation
Indices: 2075515--2075566 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
2075505 AGGGGTATCG
*
2075515 ATTCCCCATTGAATGGGTACCT
1 ATTCCCC-TTGAATGGGTACCC
2075537 ATT-CCCTTGAATGGGTACCC
1 ATTCCCCTTGAATGGGTACCC
2075557 ATTCCCCTTG
1 ATTCCCCTTG
2075567 CCCAGAAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 16 0.57
21 9 0.32
22 3 0.11
ACGTcount: A:0.19, C:0.31, G:0.17, T:0.33
Consensus pattern (21 bp):
ATTCCCCTTGAATGGGTACCC
Found at i:2076465 original size:11 final size:11
Alignment explanation
Indices: 2076431--2076466 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
2076421 CATGAATTCA
2076431 GCTGCATTATT
1 GCTGCATTATT
*
2076442 GCAGCACTTATT
1 GCTGCA-TTATT
2076454 GCTGCATTATT
1 GCTGCATTATT
2076465 GC
1 GC
2076467 ATCCCGTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.39
Consensus pattern (11 bp):
GCTGCATTATT
Found at i:2076694 original size:8 final size:9
Alignment explanation
Indices: 2076664--2076701 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
2076654 AGGTAAGTTT
2076664 TTTTAATTA
1 TTTTAATTA
2076673 TTTTAATTA
1 TTTTAATTA
*
2076682 GTTT-ATTA
1 TTTTAATTA
2076690 TTTTAAATTA
1 TTTT-AATTA
2076700 TT
1 TT
2076702 AGTTTGTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 12 0.48
10 6 0.24
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTAATTA
Found at i:2076823 original size:28 final size:27
Alignment explanation
Indices: 2076784--2076836 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
2076774 ATATTAAAAA
2076784 AATAATTAATTAGTGTGTTAGTTAGTCT
1 AATAATTAATTAGTGTG-TAGTTAGTCT
* *
2076812 AATATTTAATTAGTTTGTAGTTAGT
1 AATAATTAATTAGTGTGTAGTTAGT
2076837 TAAATAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (27 bp):
AATAATTAATTAGTGTGTAGTTAGTCT
Found at i:2076842 original size:27 final size:29
Alignment explanation
Indices: 2076783--2076847 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
2076773 TATATTAAAA
2076783 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
* *
2076812 -AATATTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
2076838 AAATAGTTAA
1 AAATAATTAA
2076848 ATTATATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.03
27 16 0.50
28 15 0.47
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (29 bp):
AAATAATTAATTAGTGTGTTAGTTAGTCT
Found at i:2077067 original size:21 final size:21
Alignment explanation
Indices: 2077042--2077081 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2077032 GTTAATTAGT
2077042 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
2077063 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAGTTATAT
2077082 CATATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:2077258 original size:29 final size:29
Alignment explanation
Indices: 2077221--2077277 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
2077211 GCAGAAACTT
*
2077221 CAAGCTCGCCCGGATGCCATGGTGACCTC
1 CAAGCTCGCCCGGATGCCATGGCGACCTC
* *
2077250 CAAGGTCGCCCGGATGGCATGGCGACCT
1 CAAGCTCGCCCGGATGCCATGGCGACCT
2077278 ACGGCAACAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.18, C:0.35, G:0.32, T:0.16
Consensus pattern (29 bp):
CAAGCTCGCCCGGATGCCATGGCGACCTC
Found at i:2080133 original size:2 final size:2
Alignment explanation
Indices: 2080126--2080156 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2080116 GCAAGAACAC
2080126 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2080157 TGTAAGATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2085470 original size:28 final size:26
Alignment explanation
Indices: 2085430--2085506 Score: 75
Period size: 26 Copynumber: 2.8 Consensus size: 26
2085420 AATTTCGGTT
2085430 AATTTTTTGAATTAATCAAAAAAAATTAA
1 AATTTTTT-AATTAAT--AAAAAAATTAA
* * *
2085459 AATTTTCTAATTTATATAAAAATTAA
1 AATTTTTTAATTAATAAAAAAATTAA
*
2085485 ATATTTTTTAATTCA-AAAAAAA
1 A-ATTTTTTAATTAATAAAAAAA
2085507 GGTTTCTATT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
26 17 0.41
27 11 0.27
28 6 0.15
29 7 0.17
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (26 bp):
AATTTTTTAATTAATAAAAAAATTAA
Found at i:2085505 original size:26 final size:25
Alignment explanation
Indices: 2085441--2085506 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 25
2085431 ATTTTTTGAA
2085441 TTAA-TCAAAAAAAATTAAAATTTT
1 TTAATTCAAAAAAAATTAAAATTTT
* * *
2085465 CTAATTTATATAAAAATTAAATATTTT
1 TTAATTCA-AAAAAAATTAAA-ATTTT
2085492 TTAATTCAAAAAAAA
1 TTAATTCAAAAAAAA
2085507 GGTTTCTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
24 3 0.09
25 2 0.06
26 17 0.52
27 11 0.33
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (25 bp):
TTAATTCAAAAAAAATTAAAATTTT
Found at i:2085506 original size:27 final size:26
Alignment explanation
Indices: 2085447--2085506 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
2085437 TGAATTAATC
*
2085447 AAAAAAAATTAAAATTTTCTAATTTA
1 AAAAAAAATTAAAATTTTCTAATTCA
* * *
2085473 TATAAAAATTAAATATTTTTTAATTCA
1 AAAAAAAATTAAA-ATTTTCTAATTCA
2085500 AAAAAAA
1 AAAAAAA
2085507 GGTTTCTATT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 11 0.41
27 16 0.59
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (26 bp):
AAAAAAAATTAAAATTTTCTAATTCA
Found at i:2086614 original size:20 final size:21
Alignment explanation
Indices: 2086589--2086640 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
2086579 TTTTCCCAAT
*
2086589 TCGCAATGCGAATAAG-TAAA
1 TCGCAATGCGAATAAGAAAAA
* **
2086609 TCGCAACGCGAATTGGAAAAA
1 TCGCAATGCGAATAAGAAAAA
2086630 TCGCAATGCGA
1 TCGCAATGCGA
2086641 TACTTACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATAAGAAAAA
Found at i:2086707 original size:20 final size:20
Alignment explanation
Indices: 2086684--2086723 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2086674 CAATGAGATA
2086684 CTGACTTTCGCAACGCGATT
1 CTGACTTTCGCAACGCGATT
2086704 CTGACTTTCGCAACGCGATT
1 CTGACTTTCGCAACGCGATT
2086724 TACATAGCGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (20 bp):
CTGACTTTCGCAACGCGATT
Found at i:2087323 original size:19 final size:19
Alignment explanation
Indices: 2087296--2087445 Score: 175
Period size: 19 Copynumber: 8.1 Consensus size: 19
2087286 GAAACCAAAA
*
2087296 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
2087315 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
2087334 TCGCGTTGCAATTTTCATT
1 TCGCGTTGCGATTTTCATT
2087353 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2087372 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
2087386 TCTCGTTGCGATAATCATT
1 TCGCGTTGCGATTTTCATT
* *
2087405 TCGCATTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
2087424 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
2087444 TC
1 TC
2087446 AACCAAAAGA
Statistics
Matches: 111, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
14 10 0.09
16 2 0.02
17 3 0.03
19 80 0.72
20 16 0.14
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2087360 original size:38 final size:38
Alignment explanation
Indices: 2087296--2087445 Score: 193
Period size: 38 Copynumber: 4.1 Consensus size: 38
2087286 GAAACCAAAA
2087296 TCGCATTGCGATTTTCATTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCTCGTTGCGATTTTCATT
* * *
2087334 TCGCGTTGCAATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCTCGTTGCGATTTTCATT
* **
2087372 TCGCGTTGCGA--TTC---TCTCGTTGCGATAATCATT
1 TCGCATTGCGATTTTCATTTCTCGTTGCGATTTTCATT
*
2087405 TCGCATTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT-TCTCGTTGCGATTTTCATT
2087444 TC
1 TC
2087446 AACCAAAAGA
Statistics
Matches: 95, Mismatches: 11, Indels: 11
0.81 0.09 0.09
Matches are distributed among these distances:
33 26 0.27
35 2 0.02
36 3 0.03
38 45 0.47
39 19 0.20
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (38 bp):
TCGCATTGCGATTTTCATTTCTCGTTGCGATTTTCATT
Found at i:2087404 original size:33 final size:33
Alignment explanation
Indices: 2087315--2087420 Score: 122
Period size: 33 Copynumber: 3.1 Consensus size: 33
2087305 GATTTTCATT
*
2087315 TCTCGTTGCGATTTTCATTTCGCGTTGCAATTTTC
1 TCTCGTTGCGATTTTCATTTCGCGTTGCGA--TTC
*
2087350 ATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATTC
1 ---TCTCGTTGCGATTTTCATTTCGCGTTGCGATTC
** *
2087386 TCTCGTTGCGATAATCATTTCGCATTGCGATTC
1 TCTCGTTGCGATTTTCATTTCGCGTTGCGATTC
2087419 TC
1 TC
2087421 ATTATCTCGT
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
33 31 0.50
36 3 0.05
38 28 0.45
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
TCTCGTTGCGATTTTCATTTCGCGTTGCGATTC
Found at i:2088992 original size:63 final size:63
Alignment explanation
Indices: 2088893--2089023 Score: 244
Period size: 63 Copynumber: 2.1 Consensus size: 63
2088883 GTTACGTGAT
2088893 GAGGTCAATGCCTCGCGTGAGGAGATCGGTACTCTACGCGATAACGATGATGCATGGCGTGTG
1 GAGGTCAATGCCTCGCGTGAGGAGATCGGTACTCTACGCGATAACGATGATGCATGGCGTGTG
* *
2088956 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
1 GAGGTCAATGCCTCGCGTGAGGAGATCGGTACTCTACGCGATAACGATGATGCATGGCGTGTG
2089019 GAGGT
1 GAGGT
2089024 GTCTACTTTA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.21, C:0.19, G:0.37, T:0.23
Consensus pattern (63 bp):
GAGGTCAATGCCTCGCGTGAGGAGATCGGTACTCTACGCGATAACGATGATGCATGGCGTGTG
Found at i:2089351 original size:95 final size:89
Alignment explanation
Indices: 2089190--2089376 Score: 275
Period size: 91 Copynumber: 2.0 Consensus size: 89
2089180 TAGATTGCTT
* *
2089190 AGTAAATTTATTCGGTTGCTTCCAATACTGTTAAAATGTTTATTAACACTGTGAAGTTAGTATTT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAATGTTTATTAACACTGTGAAGTTAGTATTT
2089255 GTCTTTTTGTTTTGTCTTTTGGTTGA
66 GTC--TTTGTTTTGTCTTTTGGTTGA
* * *
2089281 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAA--ATGT-TT-ATTAACACTGTGAAGTTAGT
2089346 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
62 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
2089374 AGT
1 AGT
2089377 TTTGAAATAT
Statistics
Matches: 87, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
91 32 0.37
93 27 0.31
94 2 0.02
95 26 0.30
ACGTcount: A:0.22, C:0.11, G:0.19, T:0.48
Consensus pattern (89 bp):
AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAATGTTTATTAACACTGTGAAGTTAGTATTT
GTCTTTGTTTTGTCTTTTGGTTGA
Found at i:2089672 original size:21 final size:21
Alignment explanation
Indices: 2089648--2089714 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2089638 TCATTCCTCG
2089648 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
2089669 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
2089690 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
2089711 AGAG
1 AGAG
2089715 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:2089672 original size:42 final size:42
Alignment explanation
Indices: 2089596--2089714 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
2089586 GACTCGCCTG
* * * * * * *
2089596 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
2089638 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
2089680 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
2089715 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:2091091 original size:14 final size:14
Alignment explanation
Indices: 2091072--2091105 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
2091062 TGTTTAATTT
2091072 ATTTGTAAAAGGTG
1 ATTTGTAAAAGGTG
*
2091086 ATTTGTAAAAGTTG
1 ATTTGTAAAAGGTG
2091100 ATTTGT
1 ATTTGT
2091106 TTAATTGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (14 bp):
ATTTGTAAAAGGTG
Found at i:2091256 original size:33 final size:33
Alignment explanation
Indices: 2091211--2091300 Score: 135
Period size: 33 Copynumber: 2.7 Consensus size: 33
2091201 AAAAAGTACT
* *
2091211 ATCGCAATGCGAAATGAAAATCGCACCGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
2091244 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* * *
2091277 AACGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
2091301 GTTGCGATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:2091270 original size:19 final size:19
Alignment explanation
Indices: 2091211--2091271 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
2091201 AAAAAGTACT
*
2091211 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
2091230 ATCGC-AC-CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
2091244 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
2091263 ATCGCAACG
1 ATCGCAACG
2091272 AGAGAAACGC
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 8 0.24
15 3 0.09
16 2 0.06
17 2 0.06
18 2 0.06
19 17 0.50
ACGTcount: A:0.43, C:0.23, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:2091318 original size:19 final size:19
Alignment explanation
Indices: 2091296--2091446 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
2091286 CGAAATTAAA
2091296 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
2091315 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
2091330 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
2091348 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
2091362 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
2091381 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
2091396 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
2091414 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
2091433 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
2091447 AGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 45 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:2091342 original size:33 final size:32
Alignment explanation
Indices: 2091300--2091426 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
2091290 ATTAAATTCG
2091300 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
2091333 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
2091366 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
2091399 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2091427 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:2091373 original size:66 final size:66
Alignment explanation
Indices: 2091293--2091425 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
2091283 ACGCGAAATT
*
2091293 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
2091358 G
66 G
*
2091359 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
2091424 G
66 G
2091425 A
1 A
2091426 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:2093733 original size:12 final size:12
Alignment explanation
Indices: 2093716--2093740 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2093706 TCTTCGGGGA
2093716 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2093728 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2093740 C
1 C
2093741 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2095050 original size:20 final size:20
Alignment explanation
Indices: 2095025--2095102 Score: 138
Period size: 20 Copynumber: 3.9 Consensus size: 20
2095015 ATTAATTTGA
2095025 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
2095045 CTATCGCAACACGAAAATGG
1 CTATCGCAACGCGAAAATGG
2095065 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
2095085 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
2095103 CGCAATGCGA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:2095143 original size:19 final size:18
Alignment explanation
Indices: 2095121--2095188 Score: 81
Period size: 19 Copynumber: 3.9 Consensus size: 18
2095111 GAAATGAAAA
2095121 TTGCATTGCGATTTTC--
1 TTGCATTGCGATTTTCAT
*
2095137 -T-CGTTGCGATTTTCAT
1 TTGCATTGCGATTTTCAT
2095153 TTCGCATTGCGATTTTCAT
1 TT-GCATTGCGATTTTCAT
2095172 TTCGCATTGCGATTTTC
1 TT-GCATTGCGATTTTC
2095189 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 12 0.27
15 1 0.02
17 1 0.02
19 31 0.69
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.49
Consensus pattern (18 bp):
TTGCATTGCGATTTTCAT
Found at i:2095145 original size:14 final size:16
Alignment explanation
Indices: 2095125--2095198 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
2095115 TGAAAATTGC
2095125 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
2095140 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
2095157 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
2095176 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
2095192 -TTGCGAT
1 ATTGCGAT
2095199 AGCCATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:2095164 original size:52 final size:53
Alignment explanation
Indices: 2095102--2095216 Score: 126
Period size: 52 Copynumber: 2.2 Consensus size: 53
2095092 AACGAGAAAA
* ***
2095102 TCGCAATGCGAAATGAAAATT-GCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATTCGCATTGCGATTTTCTCGTTGCGATAGCCATT
* *** *
2095154 TCGCATTGCG-ATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGAAATGAAAATTCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
2095206 TCGCGTTGCGA
1 TCGCATTGCGA
2095217 TAGTCTGTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
51 5 0.10
52 46 0.90
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (53 bp):
TCGCATTGCGAAATGAAAATTCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:2095324 original size:14 final size:14
Alignment explanation
Indices: 2095305--2095341 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2095295 CATCAATTAA
2095305 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2095319 ACAAATCATCTTTT
1 ACAAATCAACATTT
2095333 ACAAATCAA
1 ACAAATCAA
2095342 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2097239 original size:20 final size:19
Alignment explanation
Indices: 2097204--2097270 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
2097194 GAAACTTAAA
2097204 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
2097223 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
2097243 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
2097262 ATCGCAACG
1 ATCGCAACG
2097271 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:2097278 original size:14 final size:14
Alignment explanation
Indices: 2097259--2097314 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
2097249 ATGCGAAATG
2097259 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2097273 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
2097289 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
2097305 AAAATCGCAA
1 AAAATCGCAA
2097315 TGCGAAACAC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 19 0.53
16 8 0.22
18 9 0.25
ACGTcount: A:0.50, C:0.25, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2097301 original size:32 final size:33
Alignment explanation
Indices: 2097243--2097321 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
2097233 GGAAATGGCT
2097243 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
2097276 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2097308 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
2097322 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:2097369 original size:14 final size:14
Alignment explanation
Indices: 2097350--2097407 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
2097340 TTTCATTTCG
2097350 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2097364 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
2097380 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
2097396 CGTTGTGATTTT
1 CGTTGCGATTTT
2097408 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2097414 original size:33 final size:33
Alignment explanation
Indices: 2097333--2097423 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
2097323 ACAAATCGCA
*
2097333 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
2097366 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
2097398 TTGTGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
2097424 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:2097462 original size:20 final size:20
Alignment explanation
Indices: 2097408--2097445 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2097398 TTGTGATTTT
*
2097408 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
2097427 CATTTCCGCGTTGCGATAG
1 CATTTCCGCGTTGCGATAG
2097446 TCGTTTTCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.32
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:2097966 original size:18 final size:18
Alignment explanation
Indices: 2097940--2097984 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
2097930 GTCGATCAGA
*
2097940 TGATGGCTCTGGGTAAGG
1 TGATGGCTCTGGGCAAGG
* *
2097958 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCAAGG
2097976 TGATGGCTC
1 TGATGGCTC
2097985 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCAAGG
Found at i:2099335 original size:20 final size:20
Alignment explanation
Indices: 2099301--2099356 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
2099291 AATAGTTTCT
*
2099301 GAAAATGA-AATCGCAACAC
1 GAAAATGACTATCGCAACAC
*
2099320 GAAAATGACTATCGC-ACGC
1 GAAAATGACTATCGCAACAC
**
2099339 GAATTTGACTATCGCAAC
1 GAAAATGACTATCGCAAC
2099357 GAGAGAATCG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 24 0.77
20 7 0.23
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.18
Consensus pattern (20 bp):
GAAAATGACTATCGCAACAC
Found at i:2099642 original size:22 final size:22
Alignment explanation
Indices: 2099616--2099659 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2099606 GATGGAGATA
2099616 GACGGATTTCGCCAGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
* *
2099638 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
2099660 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGGG
Found at i:2099872 original size:20 final size:20
Alignment explanation
Indices: 2099847--2099899 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
2099837 GATTATGTAT
*
2099847 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
2099867 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
2099887 TATCTCGTTGCGA
1 TATCGCGTTGCGA
2099900 TTTTGTATTA
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:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:2099912 original size:41 final size:42
Alignment explanation
Indices: 2099867--2099961 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 42
2099857 CGAAAGTCAG
* * * *
2099867 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-GTAT
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCCTAA
* * * *
2099908 TATCGCATTACGATAGTCAGTATCGCATTGCGATTTTCCTAA
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCCTAA
2099950 T-TCGCGTTGCGA
1 TATCGCGTTGCGA
2099962 TTTACTTATT
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
41 40 0.93
42 3 0.07
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (42 bp):
TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCCTAA
Found at i:2099974 original size:20 final size:20
Alignment explanation
Indices: 2099930--2100021 Score: 148
Period size: 20 Copynumber: 4.5 Consensus size: 20
2099920 ATAGTCAGTA
* *
2099930 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGA-TTTACTTAT
*
2099951 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
2099971 TCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
2099991 TCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
2100011 TCGCATTGCGA
1 TCGCATTGCGA
2100022 ATTGGGAAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
20 57 0.85
21 10 0.15
ACGTcount: A:0.18, C:0.22, G:0.17, T:0.42
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:2100543 original size:13 final size:13
Alignment explanation
Indices: 2100525--2100549 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2100515 GATCATTTTA
2100525 TCATTTTAGAGTT
1 TCATTTTAGAGTT
2100538 TCATTTTAGAGT
1 TCATTTTAGAGT
2100550 AAAAAGGCCC
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:0.08, G:0.16, T:0.52
Consensus pattern (13 bp):
TCATTTTAGAGTT
Found at i:2101523 original size:26 final size:24
Alignment explanation
Indices: 2101461--2101523 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
2101451 CATTTTAATC
2101461 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
2101485 AAAATATAT-TTATTAATAT-TTCT
1 AAAATATATATTATTAAAATATT-T
2101508 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
2101524 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:2101525 original size:22 final size:23
Alignment explanation
Indices: 2101495--2101541 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
2101485 AAAATATATT
2101495 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
2101518 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
2101540 TA
1 TA
2101542 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:2101942 original size:19 final size:19
Alignment explanation
Indices: 2101918--2101965 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
2101908 TCTACAATTG
2101918 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
2101937 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
2101956 TCGTTGCGAT
1 TCGTTGCGAT
2101966 AGTTAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.42
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:2102702 original size:22 final size:22
Alignment explanation
Indices: 2102674--2102726 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
2102664 AATTTGGAAA
2102674 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * *
2102696 ATCGCAACAACAATTGTATACT
1 ATCGCAACGACAACTGTAGACT
2102718 ATCGCAACG
1 ATCGCAACG
2102727 CGAAATGCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.38, C:0.26, G:0.15, T:0.21
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:2103177 original size:14 final size:13
Alignment explanation
Indices: 2103155--2103193 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
2103145 CAAACATCGT
2103155 AAAACGTTTTCCTG
1 AAAACGTTTTCC-G
*
2103169 AAAATGTTTTCCG
1 AAAACGTTTTCCG
2103182 AAAAACGTTTTC
1 -AAAACGTTTTC
2103194 AGTAACAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 1 0.05
14 21 0.95
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (13 bp):
AAAACGTTTTCCG
Found at i:2103762 original size:2 final size:2
Alignment explanation
Indices: 2103755--2103792 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2103745 CTAACATAAG
2103755 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2103793 CTTTTTTTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2105804 original size:20 final size:20
Alignment explanation
Indices: 2105779--2105892 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
2105769 AATTGGGAAA
*
2105779 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
2105799 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * * *
2105819 ATCACAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
2105840 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
2105860 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
2105880 TTCGCAACGCGAT
1 ATCGCAACGCGAT
2105893 TTACATAGCG
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.80
21 12 0.15
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Done.