Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008736.1 Hibiscus syriacus cultivar Beakdansim tig00111810_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: 2478687
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 13
Found at i:223369 original size:20 final size:20
Alignment explanation
Indices: 223344--223458 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
223334 AATTGGGAAA
*
223344 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
223364 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
223385 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
223405 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
223425 TTCGCAACGTGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
223445 TTCGCAACGAGATA
1 ATCGCAACGCGATA
223459 ATACATAATC
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.03
20 62 0.78
21 13 0.16
22 2 0.03
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:223417 original size:41 final size:41
Alignment explanation
Indices: 223341--223472 Score: 133
Period size: 41 Copynumber: 3.2 Consensus size: 41
223331 GCGAATTGGG
* * * *
223341 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATAATAC
* *
223382 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATAAT-AC
** * * *
223424 --TTTCGCAACGTGATTCTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATAATAC
*
223463 ATAATCGCAA
1 AAAATCGCAA
223473 TGCGATTTTC
Statistics
Matches: 73, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
39 2 0.03
40 30 0.41
41 39 0.53
42 2 0.03
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTTTCGCAACGCGATAATAC
Found at i:223674 original size:22 final size:22
Alignment explanation
Indices: 223646--223689 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
223636 CACTCTCTCA
223646 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
223668 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
223690 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:223978 original size:20 final size:20
Alignment explanation
Indices: 223953--223990 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
223943 CGATTCTCTC
223953 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
223973 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
223991 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:224181 original size:25 final size:24
Alignment explanation
Indices: 224127--224181 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
224117 TGTTTATTAT
* *
224127 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
224151 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
224177 TGTTT
1 TGTTT
224182 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:225332 original size:18 final size:18
Alignment explanation
Indices: 225311--225355 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
225301 TCCACTTCGG
*
225311 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
225329 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
225347 GAGCCATCA
1 GAGCCATCA
225356 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:225865 original size:20 final size:21
Alignment explanation
Indices: 225842--225897 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
225832 CGCAACACAA
225842 AAATGACTATCGCAACGTG-G
1 AAATGACTATCGCAACGTGCG
*
225862 AAATGGCTATCGCAA--TGCG
1 AAATGACTATCGCAACGTGCG
**
225881 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
225898 ACAAAATCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
18 2 0.07
19 13 0.45
20 14 0.48
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (21 bp):
AAATGACTATCGCAACGTGCG
Found at i:225905 original size:14 final size:14
Alignment explanation
Indices: 225886--225943 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
225876 ATGCGAAATG
225886 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
225900 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
225916 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
225932 AAAATCGCAACG
1 AAAATCGCAACG
225944 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:225928 original size:32 final size:33
Alignment explanation
Indices: 225870--225960 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
225860 GGAAATGGCT
*
225870 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
225903 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
225935 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
225961 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:225954 original size:19 final size:18
Alignment explanation
Indices: 225870--225965 Score: 75
Period size: 19 Copynumber: 5.6 Consensus size: 18
225860 GGAAATGGCT
225870 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
225889 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATGAAA
225903 ATCGCAACGCGAAATG-AA
1 ATCGCAA-GCGAAATGAAA
*
225921 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATGAAA
225935 ATCGCAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
225954 ATCGCAATGCGA
1 ATCGCAA-GCGA
225966 TTTGTGTTTC
Statistics
Matches: 61, Mismatches: 5, Indels: 22
0.69 0.06 0.25
Matches are distributed among these distances:
14 20 0.33
15 1 0.02
16 6 0.10
17 2 0.03
18 11 0.18
19 21 0.34
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:225995 original size:18 final size:18
Alignment explanation
Indices: 225972--226096 Score: 123
Period size: 18 Copynumber: 6.9 Consensus size: 18
225962 GCGATTTGTG
225972 TTTCGCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTCA
225990 TTTCGCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTCA
*
226008 TTTCGCTTTGCGATTT--
1 TTTCGCGTTGCGATTTCA
*
226024 TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGA-TTTCA
* **
226041 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGAT-TTCA
*
226060 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCGTTGCGAT-TTCA
226080 TTTTCGCGTTGCGATTT
1 -TTTCGCGTTGCGATTT
226097 TAAGTTTCGT
Statistics
Matches: 89, Mismatches: 10, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
14 7 0.08
15 3 0.03
16 2 0.02
17 2 0.02
18 34 0.38
19 13 0.15
20 25 0.28
21 3 0.03
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (18 bp):
TTTCGCGTTGCGATTTCA
Found at i:226104 original size:20 final size:19
Alignment explanation
Indices: 225972--226113 Score: 118
Period size: 20 Copynumber: 7.7 Consensus size: 19
225962 GCGATTTGTG
225972 TTTCGCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTCA
225990 TTTCGCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTCA
*
226008 TTTCGCTTTGCGA-TTT--
1 TTTCGCGTTGCGATTTTCA
*
226024 TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* ***
226041 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGATTTTCA
**
226060 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCGTTGCGATTTTCA
*
226080 TTTTCGCGTTGCGATTTTAA
1 -TTTCGCGTTGCGATTTTCA
*
226100 GTTTCGTGTTGCGA
1 -TTTCGCGTTGCGA
226114 AAGTAAACTA
Statistics
Matches: 102, Mismatches: 15, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
14 7 0.07
15 3 0.03
16 2 0.02
17 2 0.02
18 33 0.32
19 13 0.13
20 39 0.38
21 3 0.03
ACGTcount: A:0.13, C:0.20, G:0.23, T:0.44
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:227981 original size:14 final size:14
Alignment explanation
Indices: 227962--227997 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
227952 ATTGTTTAAT
227962 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
227976 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
227990 TGATTTGT
1 TGATTTGT
227998 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:228136 original size:19 final size:19
Alignment explanation
Indices: 228114--228200 Score: 130
Period size: 19 Copynumber: 4.8 Consensus size: 19
228104 ATCGCAACGA
228114 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
228133 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
228152 GAAAATCGCAATGGGAAAT
1 GAAAATCGCAATGCGAAAT
228171 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
228185 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
228201 TTTTCATTTC
Statistics
Matches: 63, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
14 11 0.17
15 1 0.02
16 2 0.03
17 1 0.02
19 48 0.76
ACGTcount: A:0.47, C:0.16, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:228244 original size:20 final size:20
Alignment explanation
Indices: 228219--228276 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
228209 TCGCATTGCG
*
228219 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
228239 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
228259 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
228277 TCAAATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:229360 original size:24 final size:24
Alignment explanation
Indices: 229333--229386 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
229323 GTATTCGAAA
* *
229333 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
229357 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
229381 TTTGAT
1 TTTGAT
229387 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:231899 original size:19 final size:19
Alignment explanation
Indices: 231877--231935 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
231867 GGAAATTACT
231877 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
231896 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
231910 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
231929 ATCGCAA
1 ATCGCAA
231936 CGCTAATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:232081 original size:14 final size:14
Alignment explanation
Indices: 232062--232098 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
232052 CATCAATTAA
232062 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
232076 ACAAATCACCTTTT
1 ACAAATCAACTTTT
232090 ACAAATCAA
1 ACAAATCAA
232099 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:233330 original size:27 final size:27
Alignment explanation
Indices: 233289--233344 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
233279 GCGGTCTTAG
233289 CCCAAAGGGTATTATCCAGAATTGTGT
1 CCCAAAGGGTATTATCCAGAATTGTGT
*
233316 CCCAAAGGGTGTTATCCAGAATTGTGT
1 CCCAAAGGGTATTATCCAGAATTGTGT
233343 CC
1 CC
233345 GGTAGTTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (27 bp):
CCCAAAGGGTATTATCCAGAATTGTGT
Found at i:233548 original size:21 final size:21
Alignment explanation
Indices: 233482--233548 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
233472 GTGAATCGGG
*
233482 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
233502 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
233524 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
233545 CTCT
1 CTCT
233549 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:235691 original size:33 final size:33
Alignment explanation
Indices: 235634--235732 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
235624 ACGAGATAAT
*
235634 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
235668 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
235701 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
235733 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:235726 original size:19 final size:19
Alignment explanation
Indices: 235609--235793 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
235599 TCTTTTGGTT
*
235609 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
235628 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
235648 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
235666 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
235682 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
235700 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
235715 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
235735 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
235754 GAAATGAAAATCGCAACGT
1 GAAATGAAAATCGCAACGC
*
235773 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
235792 GA
1 GA
235794 TTTTTGTTTC
Statistics
Matches: 136, Mismatches: 17, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 60 0.44
20 45 0.33
21 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:235747 original size:39 final size:38
Alignment explanation
Indices: 235704--235793 Score: 144
Period size: 39 Copynumber: 2.3 Consensus size: 38
235694 GCGACCAGAC
235704 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
* *
235743 AATCGCAACGCGAAATGAAAATCGCAACGTGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
*
235781 AATCGCAATGCGA
1 AATCGCAACGCGA
235794 TTTTTGTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 21 0.44
39 27 0.56
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:236411 original size:20 final size:20
Alignment explanation
Indices: 236386--236438 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
236376 GCGCTATGTA
236386 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
236406 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
236426 TATCTCGTTGCGA
1 AATCGCGTTGCGA
236439 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:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:236472 original size:20 final size:20
Alignment explanation
Indices: 236447--236500 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
236437 GATTTTGTAT
236447 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
236467 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
236487 TATCGCATTGCGAT
1 TATCGCATTGCGAT
236501 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:236485 original size:61 final size:61
Alignment explanation
Indices: 236387--236503 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
236377 CGCTATGTAA
* * * * *
236387 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
236448 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
236504 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:236519 original size:61 final size:61
Alignment explanation
Indices: 236387--236521 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
236377 CGCTATGTAA
* * * * * ** *
236387 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
236448 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
236510 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
236522 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:237866 original size:23 final size:23
Alignment explanation
Indices: 237840--237906 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
237830 GAACATGACG
*
237840 GCGGATCAGTTAGAGTAGAGGCA
1 GCGGATCAGTTGGAGTAGAGGCA
*
237863 GCGGAGT-AGTTGGAGTAGAGGCG
1 GCGGA-TCAGTTGGAGTAGAGGCA
* *
237886 GCGAAGCAGTTGGAGTAGAGG
1 GCGGATCAGTTGGAGTAGAGG
237907 TAAAAATGGT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 37 0.97
24 1 0.03
ACGTcount: A:0.27, C:0.10, G:0.46, T:0.16
Consensus pattern (23 bp):
GCGGATCAGTTGGAGTAGAGGCA
Found at i:238552 original size:73 final size:73
Alignment explanation
Indices: 238431--238755 Score: 535
Period size: 73 Copynumber: 4.5 Consensus size: 73
238421 TATCTGGAAA
* * * *
238431 TGTTTTAAGAAAAACAATCTTAAGTGAGATAAATTACTATTTCGAGTGAAACTTTCTCAAGTGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCGAG
238496 AAAAAGTT
66 AAAAAGTT
*
238504 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTTCAAGTGAAACTTTCTCAAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCGAG
*
238569 AAAAAATT
66 AAAAAGTT
*
238577 TGTTTTAAGAAAAATAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCGAG
238642 AAAAAGTT
66 AAAAAGTT
* *
238650 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAATGAAACTTTCTCTAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCGAG
238715 AAACAA-TT
66 AAA-AAGTT
* *
238723 TATTTTAAGAAAAACAATCTCAAGCGAGATAAA
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
238756 ATTTATTTGA
Statistics
Matches: 237, Mismatches: 14, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
73 235 0.99
74 2 0.01
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.31
Consensus pattern (73 bp):
TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCGAG
AAAAAGTT
Found at i:239259 original size:177 final size:176
Alignment explanation
Indices: 238998--239315 Score: 521
Period size: 177 Copynumber: 1.8 Consensus size: 176
238988 TGAAAACCAA
* *
238998 GCTTAGTTTATTGGTTGTCAATGAACCCCTTAAAAGGCTTAGCTTCCTTTAACAGCTCTTTTGAG
1 GCTTAGTTTATTAGTTGTCAAGGAACCCCTTAAAAGGCTTAGCTTCCTTTAACAGCTCTTTTGAG
* * *
239063 ATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTTGAAAACATTCTGCACTGAAGG
66 ATAATTAGTAAACCCCCGAAGACTTGGTTTCTAAAATCTCATTTGAAAACATCCTACACTGAAGG
*
239128 TCTTATGGATGACCCATAAGACTTATGAATCAAGAAACACTCGAAG
131 TCTTATAGATGACCCATAAGACTTATGAATCAAGAAACACTCGAAG
* **
239174 GCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAA-GCTTAGCTTCCTTTAACAGCTCTTTTG
1 GCTTAGTTTATTAGTTGTCAAGGAACCCC-TT-AAAAGGCTTAGCTTCCTTTAACAGCTCTTTTG
*
239238 AGATAATTAGTAAAGCCCCGAAGACTTGGTTTCTAAAATCTCATTTGAAAACATCCTACACTGAA
64 AGATAATTAGTAAACCCCCGAAGACTTGGTTTCTAAAATCTCATTTGAAAACATCCTACACTGAA
239303 GGTCTTATAGATG
129 GGTCTTATAGATG
239316 GCCCGGAGGT
Statistics
Matches: 130, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
176 26 0.20
177 102 0.78
178 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (176 bp):
GCTTAGTTTATTAGTTGTCAAGGAACCCCTTAAAAGGCTTAGCTTCCTTTAACAGCTCTTTTGAG
ATAATTAGTAAACCCCCGAAGACTTGGTTTCTAAAATCTCATTTGAAAACATCCTACACTGAAGG
TCTTATAGATGACCCATAAGACTTATGAATCAAGAAACACTCGAAG
Found at i:239689 original size:174 final size:176
Alignment explanation
Indices: 239397--239716 Score: 536
Period size: 174 Copynumber: 1.8 Consensus size: 176
239387 TAAAAATCAA
* * *
239397 GCTTAGTTTCTTGGTTGTCAAGGAACCCCTTAAAAGGCTTAGCTTCCTTTAACAACTCTTTTGAG
1 GCTTAGTTTCTTAGTTGTCAAGGAA-CCCTTAAAAGACTTAGCTTCATTTAACAACTCTTTTGAG
239462 ATAATTAGTAAACCCCCGAAGGCTGGGTTTCTAAAATCTCATTTGAAAACATCCTGCACTG-AAG
65 ATAATTAGTAAACCCCCGAAGGCTGGGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAAG
239526 GTCTTATGGATGGCCCATATGACTTACGAATCAAGAAACCCACGAAG
130 GTCTTATGGATGGCCCATATGACTTACGAATCAAGAAACCCACGAAG
*** *
239573 GCTTAGTTTCTTAGTTGTCAAGGAA-CCTTGTTAGACTTAGCTTCATTTAACAGCTCTTTTGAGA
1 GCTTAGTTTCTTAGTTGTCAAGGAACCCTTAAAAGACTTAGCTTCATTTAACAACTCTTTTGAGA
* *
239637 TAATTAGTAAAGCCCCGAAGGCTTGGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAAGG
66 TAATTAGTAAACCCCCGAAGGCTGGGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAAGG
239702 TCTTATGGATGGCCC
131 TCTTATGGATGGCCC
239717 GGAGGTCTTA
Statistics
Matches: 134, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
174 91 0.68
175 19 0.14
176 24 0.18
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (176 bp):
GCTTAGTTTCTTAGTTGTCAAGGAACCCTTAAAAGACTTAGCTTCATTTAACAACTCTTTTGAGA
TAATTAGTAAACCCCCGAAGGCTGGGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAAGG
TCTTATGGATGGCCCATATGACTTACGAATCAAGAAACCCACGAAG
Found at i:239849 original size:397 final size:398
Alignment explanation
Indices: 238854--239939 Score: 1804
Period size: 399 Copynumber: 2.7 Consensus size: 398
238844 TTTCTAAAAT
*
238854 CCCCGAAGGCTTGGTTTCTAAAATCTCATTTGAAAACATCTTGCACTGAAGGTCTTATGGATGGC
1 CCCCGAAGGCTTGGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGC
* * * * * *
238919 CCGTAGGACTTATTATCTTGCTGAAAAAGCTTACAGATGACCCGGAGGATTTAAACATCAAGAAA
66 CCGGAGGTCTTATCATCTTGCTCAGAAGGCTTACAGATGACCCGGAGGATTTAAACATCAAGAAA
* * *
238984 CTCTTGAAAACCAAGCTTAGTTTATTGGTTGTCAATGAACCCCTTAAAAGGCTTAGCTTCCTTTA
131 CTCTTGAAAATCAAGCTTAGTTTCTTGGTTGTCAAGGAACCCCTTAAAAGGCTTAGCTTCCTTTA
*
239049 ACAGCTCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTTGAAAACA
196 ACAACTCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTTGAAAACA
* * * *
239114 TTCTGCACTGAAGGTCTTATGGATGACCCATAAGACTTATGAATCAAGAAACACTCGAAGGCTTA
261 TCCTGCACTGAAGGTCTTATGGATGGCCCATAAGACTTACGAATCAAGAAACACACGAAGGCTTA
*
239179 GTTTCTTAGTTGTCAAGGAACCCCTTTGTTAAGCTTAGCTTCCTTTAACAGCTCTTTTGAGATAA
326 GTTTCTTAGTTGTCAAGGAA-CCCTTTGTTAAGCTTAGCTTCATTTAACAGCTCTTTTGAGATAA
239244 TTAGTAAAG
390 TTAGTAAAG
* * *
239253 CCCCGAAGACTTGGTTTCTAAAATCTCATTTGAAAACATCCTACACTGAAGGTCTTATAGATGGC
1 CCCCGAAGGCTTGGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGC
* *
239318 CCGGAGGTCTTATCATCTTTCTCAGAAGGCTTACAGATGACACGGAGGATTTAAACATCAAGAAA
66 CCGGAGGTCTTATCATCTTGCTCAGAAGGCTTACAGATGACCCGGAGGATTTAAACATCAAGAAA
*
239383 CTCTTAAAAATCAAGCTTAGTTTCTTGGTTGTCAAGGAACCCCTTAAAAGGCTTAGCTTCCTTTA
131 CTCTTGAAAATCAAGCTTAGTTTCTTGGTTGTCAAGGAACCCCTTAAAAGGCTTAGCTTCCTTTA
*
239448 ACAACTCTTTTGAGATAATTAGTAAACCCCCGAAGGCTGGGTTTCTAAAATCTCATTTGAAAACA
196 ACAACTCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTTGAAAACA
* *
239513 TCCTGCACTGAAGGTCTTATGGATGGCCCATATGACTTACGAATCAAGAAACCCACGAAGGCTTA
261 TCCTGCACTGAAGGTCTTATGGATGGCCCATAAGACTTACGAATCAAGAAACACACGAAGGCTTA
239578 GTTTCTTAGTTGTCAAGGAA-CC-TTGTT-AGACTTAGCTTCATTTAACAGCTCTTTTGAGATAA
326 GTTTCTTAGTTGTCAAGGAACCCTTTGTTAAG-CTTAGCTTCATTTAACAGCTCTTTTGAGATAA
239640 TTAGTAAAG
390 TTAGTAAAG
239649 CCCCGAAGGCTTGGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAAGGTCTTATGGATGG
1 CCCCGAAGGCTTGGTTTCTAAAATCTCATTTGAAAACATCCTGCACTG-AAGGTCTTATGGATGG
*
239714 CCCGGAGGTCTTATCATCTTGCTCAGAAGGCTTACAGATGACCCGAAGGATTTAAACATCAAGAA
65 CCCGGAGGTCTTATCATCTTGCTCAGAAGGCTTACAGATGACCCGGAGGATTTAAACATCAAGAA
239779 ACTCTTGAAAATCAAGCTTAGTTTCTTGGTTGTCAAGGAACCCCTTAAAAGGCTTAGCTTCCTTT
130 ACTCTTGAAAATCAAGCTTAGTTTCTTGGTTGTCAAGGAACCCCTTAAAAGGCTTAGCTTCCTTT
* * * *
239844 AACAACTCTTTTGAGATAATTAAG-AAACCACTGAAGTGCTTAGTTTCCAAAATCTCATTTGAAA
195 AACAACTCTTTTGAGATAATT-AGTAAACCCCCGAAG-GCTTGGTTTCTAAAATCTCATTTGAAA
* *
239908 ACATCCTGC-CCGGAGGTCTTATGGATGGCCCA
258 ACATCCTGCACTGAAGGTCTTATGGATGGCCCA
239940 GAGGTCTTAC
Statistics
Matches: 644, Mismatches: 39, Indels: 10
0.93 0.06 0.01
Matches are distributed among these distances:
395 2 0.00
396 91 0.14
397 195 0.30
398 35 0.05
399 321 0.50
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.30
Consensus pattern (398 bp):
CCCCGAAGGCTTGGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGC
CCGGAGGTCTTATCATCTTGCTCAGAAGGCTTACAGATGACCCGGAGGATTTAAACATCAAGAAA
CTCTTGAAAATCAAGCTTAGTTTCTTGGTTGTCAAGGAACCCCTTAAAAGGCTTAGCTTCCTTTA
ACAACTCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTTGAAAACA
TCCTGCACTGAAGGTCTTATGGATGGCCCATAAGACTTACGAATCAAGAAACACACGAAGGCTTA
GTTTCTTAGTTGTCAAGGAACCCTTTGTTAAGCTTAGCTTCATTTAACAGCTCTTTTGAGATAAT
TAGTAAAG
Found at i:240406 original size:13 final size:13
Alignment explanation
Indices: 240388--240415 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
240378 CTTCATTTAG
240388 TCAAAATGGCATT
1 TCAAAATGGCATT
240401 TCAAAATGGCATT
1 TCAAAATGGCATT
240414 TC
1 TC
240416 TGAAGAACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (13 bp):
TCAAAATGGCATT
Found at i:241085 original size:54 final size:54
Alignment explanation
Indices: 240998--241130 Score: 169
Period size: 54 Copynumber: 2.4 Consensus size: 54
240988 ATAATTACTA
* * * * *
240998 GTTCATAAAACATTTTACAACACATTCATCCTTTCCTGTGGTTTCTGCAC-AGAT
1 GTTCGTAAAACATTTAACAACACAATCATCCTTTCATGTGGCTTCTGC-CTAGAT
241052 GTTCGTAAAACATTTAACAACACAATCATCCTTTCATGTGGCTTCTGCCTAGAT
1 GTTCGTAAAACATTTAACAACACAATCATCCTTTCATGTGGCTTCTGCCTAGAT
* * *
241106 TTCTCGTAAAACATTTGATAACACA
1 GT-TCGTAAAACATTTAACAACACA
241131 TGTGAGCTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
53 1 0.01
54 48 0.70
55 20 0.29
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (54 bp):
GTTCGTAAAACATTTAACAACACAATCATCCTTTCATGTGGCTTCTGCCTAGAT
Found at i:242984 original size:13 final size:13
Alignment explanation
Indices: 242966--242999 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
242956 ACCGGTCATA
242966 ACCCGACCCGTTT
1 ACCCGACCCGTTT
242979 ACCCGACCCGTTT
1 ACCCGACCCGTTT
242992 ACCCGACC
1 ACCCGACC
243000 TGACCTGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.18, C:0.50, G:0.15, T:0.18
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:243004 original size:18 final size:18
Alignment explanation
Indices: 242983--243017 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
242973 CCGTTTACCC
*
242983 GACCCGTTTACCCGACCT
1 GACCCGTTGACCCGACCT
*
243001 GACCTGTTGACCCGACC
1 GACCCGTTGACCCGACC
243018 CGTTGACCGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.43, G:0.20, T:0.20
Consensus pattern (18 bp):
GACCCGTTGACCCGACCT
Found at i:243012 original size:13 final size:13
Alignment explanation
Indices: 242966--243025 Score: 57
Period size: 13 Copynumber: 4.2 Consensus size: 13
242956 ACCGGTCATA
*
242966 ACCCGACCCGTTT
1 ACCCGACCCGTTG
*
242979 ACCCGACCCGTTT
1 ACCCGACCCGTTG
242992 ACCCGACCTGACCTGTTG
1 ACCCGA-C---CC-GTTG
243010 ACCCGACCCGTTG
1 ACCCGACCCGTTG
243023 ACC
1 ACC
243026 GTTGACCGGC
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
13 26 0.63
14 3 0.07
17 3 0.07
18 9 0.22
ACGTcount: A:0.17, C:0.45, G:0.18, T:0.20
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:247357 original size:6 final size:6
Alignment explanation
Indices: 247343--247413 Score: 76
Period size: 6 Copynumber: 11.8 Consensus size: 6
247333 CTTGATTCAA
247343 TTTTT- TTTTTC TTTTTC TTTTTC TTTTTC TGTTTTC --TTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC T-TTTTC TTTTTC TTTTTC
* *
247389 ATCTATC TTTTTC TTTTTTC TTTTT
1 -TTTTTC TTTTTC -TTTTTC TTTTT
247414 TCATCTCTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
4 4 0.07
5 5 0.09
6 32 0.57
7 15 0.27
ACGTcount: A:0.03, C:0.15, G:0.01, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:247370 original size:13 final size:13
Alignment explanation
Indices: 247343--247413 Score: 67
Period size: 13 Copynumber: 5.3 Consensus size: 13
247333 CTTGATTCAA
247343 TTTT-TTTTTTCT
1 TTTTCTTTTTTCT
247355 TTTTC-TTTTTCT
1 TTTTCTTTTTTCT
*
247367 TTTTCTGTTTTCT
1 TTTTCTTTTTTCT
247380 TTCTT-TTTCATCTATCT
1 TT-TTCTTT--T-T-TCT
247397 TTTTCTTTTTTCT
1 TTTTCTTTTTTCT
247410 TTTT
1 TTTT
247414 TCATCTCTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
12 16 0.33
13 17 0.35
14 3 0.06
15 2 0.04
16 3 0.06
17 8 0.16
ACGTcount: A:0.03, C:0.15, G:0.01, T:0.80
Consensus pattern (13 bp):
TTTTCTTTTTTCT
Found at i:247377 original size:19 final size:18
Alignment explanation
Indices: 247343--247413 Score: 76
Period size: 17 Copynumber: 3.9 Consensus size: 18
247333 CTTGATTCAA
247343 TTTTT-TTTTTCTTTTTC
1 TTTTTCTTTTTCTTTTTC
247360 TTTTTCTTTTTCTGTTTTC
1 TTTTTCTTTTTCT-TTTTC
* *
247379 --TTTCTTTTTCATCTATC
1 TTTTTCTTTTTC-TTTTTC
247396 TTTTTCTTTTTTCTTTTT
1 TTTTTC-TTTTTCTTTTT
247414 TCATCTCTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
17 18 0.41
18 8 0.18
19 12 0.27
20 6 0.14
ACGTcount: A:0.03, C:0.15, G:0.01, T:0.80
Consensus pattern (18 bp):
TTTTTCTTTTTCTTTTTC
Found at i:247400 original size:23 final size:23
Alignment explanation
Indices: 247356--247404 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
247346 TTTTTTTCTT
* *
247356 TTTCTTTTTCTTTTTCTGTTTTC
1 TTTCTTTTTCTCTATCTGTTTTC
247379 TTTCTTTTTCATCTATCT-TTTTC
1 TTTCTTTTTC-TCTATCTGTTTTC
247402 TTT
1 TTT
247405 TTTCTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (23 bp):
TTTCTTTTTCTCTATCTGTTTTC
Found at i:247400 original size:30 final size:29
Alignment explanation
Indices: 247345--247411 Score: 89
Period size: 30 Copynumber: 2.3 Consensus size: 29
247335 TGATTCAATT
* * *
247345 TTTTTTTTCTTTTTCTTTTTCTTTTTCTG
1 TTTTCTTTCTTTTTCTCTATCTTTTTCTG
*
247374 TTTTCTTTCTTTTTCATCTATCTTTTTCTT
1 TTTTCTTTCTTTTTC-TCTATCTTTTTCTG
247404 TTTTCTTT
1 TTTTCTTT
247412 TTTCATCTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
29 14 0.42
30 19 0.58
ACGTcount: A:0.03, C:0.16, G:0.01, T:0.79
Consensus pattern (29 bp):
TTTTCTTTCTTTTTCTCTATCTTTTTCTG
Found at i:247844 original size:8 final size:8
Alignment explanation
Indices: 247827--247887 Score: 52
Period size: 8 Copynumber: 7.5 Consensus size: 8
247817 AATCAATCCC
*
247827 TCTTTCTT
1 TCTTTTTT
247835 TCTTTTTT
1 TCTTTTTT
*
247843 TCCTTTTT
1 TCTTTTTT
247851 TCTTTTTT
1 TCTTTTTT
*
247859 AT-TTCTTCT
1 -TCTT-TTTT
*
247868 TCTTCTTT
1 TCTTTTTT
*
247876 TCCTTTTT
1 TCTTTTTT
247884 TCTT
1 TCTT
247888 CTTCTTACTT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
8 35 0.85
9 6 0.15
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (8 bp):
TCTTTTTT
Found at i:247876 original size:19 final size:18
Alignment explanation
Indices: 247834--247893 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
247824 CCCTCTTTCT
*
247834 TTCTTTTTTTCCTT-TT-
1 TTCTTTTTTTTCTTCTTC
247850 TTCTTTTTTATTTCTTCTTC
1 TTC-TTTTT-TTTCTTCTTC
247870 TTCTTTTCCTTTT-TTCTTC
1 TTCTTTT--TTTTCTTCTTC
247889 TTCTT
1 TTCTT
247894 ACTTCGAGCA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
16 3 0.08
17 5 0.14
18 5 0.14
19 17 0.46
20 6 0.16
21 1 0.03
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.77
Consensus pattern (18 bp):
TTCTTTTTTTTCTTCTTC
Found at i:247882 original size:25 final size:26
Alignment explanation
Indices: 247847--247898 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
247837 TTTTTTTCCT
* *
247847 TTTTTCTTTTTTATTTCTTCTT-CTTC
1 TTTTCCTTTTTT-CTTCTTCTTACTTC
247873 TTTTCCTTTTTTCTTCTTCTTACTTC
1 TTTTCCTTTTTTCTTCTTCTTACTTC
247899 GAGCATGCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.73
Consensus pattern (26 bp):
TTTTCCTTTTTTCTTCTTCTTACTTC
Found at i:254627 original size:20 final size:21
Alignment explanation
Indices: 254602--254653 Score: 79
Period size: 20 Copynumber: 2.4 Consensus size: 21
254592 TGTTGTTGTG
254602 GTTTATGTTCATTTA-TGTTC
1 GTTTATGTTCATTTATTGTTC
254622 GTTTATGTTCATTTATTGTGTTC
1 GTTTATGTTCATTTA-T-TGTTC
254645 GTTTATGTT
1 GTTTATGTT
254654 TGTTTATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 15 0.52
23 14 0.48
ACGTcount: A:0.13, C:0.08, G:0.17, T:0.62
Consensus pattern (21 bp):
GTTTATGTTCATTTATTGTTC
Found at i:254647 original size:23 final size:23
Alignment explanation
Indices: 254602--254697 Score: 92
Period size: 23 Copynumber: 4.3 Consensus size: 23
254592 TGTTGTTGTG
254602 GTTTATGTTCATTTA---TGTTC
1 GTTTATGTTCATTTATTGTGTTC
254622 GTTTATGTTCATTTATTGTGTTC
1 GTTTATGTTCATTTATTGTGTTC
** *
254645 GTTTATGTTTGTTTATTATGTTC
1 GTTTATGTTCATTTATTGTGTTC
* * *
254668 -TCTTATGTTCGTTCATTTGTATTC
1 GT-TTATGTTCATTTA-TTGTGTTC
254692 GTTTAT
1 GTTTAT
254698 AATTTAAATG
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
20 15 0.24
22 1 0.02
23 36 0.57
24 10 0.16
25 1 0.02
ACGTcount: A:0.14, C:0.09, G:0.16, T:0.61
Consensus pattern (23 bp):
GTTTATGTTCATTTATTGTGTTC
Found at i:254653 original size:10 final size:10
Alignment explanation
Indices: 254602--254660 Score: 64
Period size: 10 Copynumber: 5.6 Consensus size: 10
254592 TGTTGTTGTG
254602 GTTTATGTTC
1 GTTTATGTTC
*
254612 ATTTATGTTC
1 GTTTATGTTC
254622 GTTTATGTTC
1 GTTTATGTTC
*
254632 ATTTATTGTGTTC
1 GTTTA---TGTTC
*
254645 GTTTATGTTT
1 GTTTATGTTC
254655 GTTTAT
1 GTTTAT
254661 TATGTTCTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
10 32 0.78
13 9 0.22
ACGTcount: A:0.14, C:0.07, G:0.17, T:0.63
Consensus pattern (10 bp):
GTTTATGTTC
Found at i:255709 original size:2 final size:2
Alignment explanation
Indices: 255697--255726 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
255687 TAAGCCACGC
255697 AT AT CAT 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
255727 CTTAAACAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:260178 original size:31 final size:31
Alignment explanation
Indices: 260132--260190 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
260122 TATGATAATG
*
260132 TTACATGAGCTATGTGATAATAAGCTATGAGA
1 TTACATGACCTATGTGAT-ATAAGCTATGAGA
*
260164 TTACATG-CCTATGTGATATAAGTTATG
1 TTACATGACCTATGTGATATAAGCTATG
260191 TGAATTGTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 9 0.36
31 9 0.36
32 7 0.28
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36
Consensus pattern (31 bp):
TTACATGACCTATGTGATATAAGCTATGAGA
Found at i:260318 original size:21 final size:22
Alignment explanation
Indices: 260269--260339 Score: 65
Period size: 21 Copynumber: 3.2 Consensus size: 22
260259 TAGTCAAGGG
* *
260269 TTCTACACGGTCATT-TGAGACA
1 TTCTACACGGTCCTTCAG-GACA
260291 TTTCTACACGGTCCTTCAGGAC-
1 -TTCTACACGGTCCTTCAGGACA
** *
260313 TTCTACGTGGTCCTTCGGGACA
1 TTCTACACGGTCCTTCAGGACA
260335 TTCTA
1 TTCTA
260340 TGTGGCACTT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 18 0.44
22 5 0.12
23 17 0.41
24 1 0.02
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.34
Consensus pattern (22 bp):
TTCTACACGGTCCTTCAGGACA
Found at i:260344 original size:22 final size:21
Alignment explanation
Indices: 260300--260352 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
260290 ATTTCTACAC
*
260300 GGTCCTTCAGGACTTCTACGT
1 GGTCCTTCGGGACTTCTACGT
*
260321 GGTCCTTCGGGACATTCTATGT
1 GGTCCTTCGGGAC-TTCTACGT
260343 GG-CACTTCGG
1 GGTC-CTTCGG
260353 TGTATTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 13 0.46
22 15 0.54
ACGTcount: A:0.13, C:0.26, G:0.28, T:0.32
Consensus pattern (21 bp):
GGTCCTTCGGGACTTCTACGT
Found at i:264316 original size:27 final size:27
Alignment explanation
Indices: 264266--264339 Score: 96
Period size: 27 Copynumber: 2.7 Consensus size: 27
264256 TGCACCTATG
264266 GTGCAATTACAGTTACAAGG-CACTAAAT
1 GTGCAA-TACAGTTA-AAGGCCACTAAAT
*
264294 GTGCAATACAGTTATAGGCCACTAAAT
1 GTGCAATACAGTTAAAGGCCACTAAAT
* *
264321 GTGCTATACAGTTACAGGC
1 GTGCAATACAGTTAAAGGC
264340 AGTTTATACT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 3 0.07
27 33 0.79
28 6 0.14
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (27 bp):
GTGCAATACAGTTAAAGGCCACTAAAT
Found at i:267246 original size:55 final size:54
Alignment explanation
Indices: 267177--267453 Score: 171
Period size: 55 Copynumber: 5.1 Consensus size: 54
267167 GGGATAAATG
* * *
267177 AGACTTGAAAAATCTTCAAATGATGA-GCCGGCTCCCTATTCCTTCAG-GAAGTATA
1 AGACTTGAACAATCTTCAAA-AAT-ATGCCGGCTCCCTATTCATTCAGAG-AGTATA
* * * *
267232 AGACTCGAACAATCTTCATAAAATATGTCTGCTCTCTATTCATTCAGAGAGTATA
1 AGACTTGAACAATCTTCA-AAAATATGCCGGCTCCCTATTCATTCAGAGAGTATA
* * *
267287 AGACTTGAACAATCTTCAATAAA-ACGGGTCC-GCTCTCTATTCCTTCAGAGAGTAT-
1 AGACTTGAACAATCTTCAA-AAATA--TG-CCGGCTCCCTATTCATTCAGAGAGTATA
* * * *
267342 AGAACTCGGAA-AATCTTCAATAAACAGGTCC-GCTCCCTATTCCTTCAGAGAGTATA
1 AG-ACT-TGAACAATCTTCAA-AAATATG-CCGGCTCCCTATTCATTCAGAGAGTATA
* * * * * *
267398 GGAC-T---CGATCTTCATAAAATGTGTCTGCTCCCTATTCCTTCAGAGAGTATA
1 AGACTTGAACAATCTTCA-AAAATATGCCGGCTCCCTATTCATTCAGAGAGTATA
*
267449 GGACT
1 AGACT
267454 CGATCTTCAA
Statistics
Matches: 187, Mismatches: 20, Indels: 33
0.78 0.08 0.14
Matches are distributed among these distances:
50 1 0.01
51 40 0.21
52 1 0.01
54 3 0.02
55 93 0.50
56 44 0.24
57 5 0.03
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (54 bp):
AGACTTGAACAATCTTCAAAAATATGCCGGCTCCCTATTCATTCAGAGAGTATA
Found at i:267349 original size:111 final size:105
Alignment explanation
Indices: 267207--267456 Score: 281
Period size: 111 Copynumber: 2.3 Consensus size: 105
267197 TGATGAGCCG
* * * *
267207 GCTCCCTATTCCTTCAG-GAAGTATA-AGACTCGAACAATCTTC-ATAAAATATGTCTGCTCTCT
1 GCTCCCTATTCCTTCAGAG-AGTATAGA-ACTCGAA-AATCTTCAAT-AAACAGGTCCGCTCCCT
267269 ATTCATTCAGAGAGTATAAGACTTGAACAATCTTCAATAAAACGGGTCC
62 ATTCATTCAGAGAGTATAAGAC-T---CAATCTTC-ATAAAACGGGTCC
*
267318 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGGAAAATCTTCAATAAACAGGTCCGCTCCCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTC-GAAAATCTTCAATAAACAGGTCCGCTCCCTATT
* * * * * *
267383 CCTTCAGAGAGTATAGGACTCGATCTTCATAAAATGTGTCT
65 CATTCAGAGAGTATAAGACTCAATCTTCATAAAACGGGTCC
*
267424 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGA
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGA
267457 TCTTCAACGA
Statistics
Matches: 122, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
105 2 0.02
106 39 0.32
107 7 0.06
110 1 0.01
111 66 0.54
112 7 0.06
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (105 bp):
GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAAATCTTCAATAAACAGGTCCGCTCCCTATTC
ATTCAGAGAGTATAAGACTCAATCTTCATAAAACGGGTCC
Found at i:267431 original size:51 final size:51
Alignment explanation
Indices: 267207--267462 Score: 239
Period size: 55 Copynumber: 4.8 Consensus size: 51
267197 TGATGAGCCG
* * *
267207 GCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTCATAAAATATGTCT
1 GCTCCCTATTCCTTCAGAG-AGTATAGGACTCG----ATCTTCATAAAATGTGTCC
* * * * * *
267262 GCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTCAATAAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGAC-T---CGATCTTC-ATAAAATGTGTCC
* *
267318 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGGAAAATCTTCAATAAACA-G-GTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTC-G---ATCTTC-ATAAA-ATGTGTCC
*
267373 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCATAAAATGTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCATAAAATGTGTCC
267424 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCA
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCA
267463 ACGAACGAGT
Statistics
Matches: 174, Mismatches: 14, Indels: 30
0.80 0.06 0.14
Matches are distributed among these distances:
49 1 0.01
50 6 0.03
51 48 0.28
52 1 0.01
54 1 0.01
55 65 0.37
56 50 0.29
57 1 0.01
59 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (51 bp):
GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCATAAAATGTGTCC
Found at i:268846 original size:7 final size:7
Alignment explanation
Indices: 268834--268869 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
268824 TTATTTCTTT
268834 TTTTTCA
1 TTTTTCA
268841 TTTTTCA
1 TTTTTCA
*
268848 TTTTTTA
1 TTTTTCA
268855 TTTTTCA
1 TTTTTCA
268862 TTTTTCA
1 TTTTTCA
268869 T
1 T
268870 CATTTTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTTCA
Found at i:268858 original size:21 final size:21
Alignment explanation
Indices: 268822--268869 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
268812 TGAACCCTCC
268822 TTTT-ATTTCTTTTTTTTCAT
1 TTTTCATTTCTTTTTTTTCAT
268842 TTTTCATTT-TTTATTTTTCAT
1 TTTTCATTTCTTT-TTTTTCAT
268863 TTTTCAT
1 TTTTCAT
268870 CATTTTTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTTCATTTCTTTTTTTTCAT
Found at i:268919 original size:13 final size:12
Alignment explanation
Indices: 268901--268930 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
268891 TTTTTTTATT
268901 TTTTTATTTCTCC
1 TTTTTATTTCT-C
268914 TTTTTATTTCTC
1 TTTTTATTTCTC
268926 TTTTT
1 TTTTT
268931 CTTTTTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTATTTCTC
Found at i:298638 original size:149 final size:146
Alignment explanation
Indices: 298362--299315 Score: 988
Period size: 149 Copynumber: 6.7 Consensus size: 146
298352 TAGATCATAT
* *
298362 TATTTCACCTGGCCTACTCCACACGTTA-AGGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACT
1 TATTTCACCCGGCCTACTCCACACGTTAGA-GCGCTCGGCGTAAGACCAGGTCATCCTGCCTACT
* * * *
298426 CCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACCCCACACGTTGAGGCGCTCGA
65 CCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACTCTACACGTTGAAGTGCTCGA
*
298491 CCTGATATTAAAGCACATTC
130 CGTGATATT--AGCACA-TC
* *
298511 TATTTCACCCGACCTACTCCACACGTTAGGGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTC
1 TATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTC
* * * *
298576 CCCTCTAGAAGCGCTCGGCATGAACTCTGTCTACCCTCCCTACCCTACACGTTG-AGATGCTCGG
66 CCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACTCTACACGTTGAAG-TGCTCGA
*
298640 CGTGA-A-T----C-TGG
130 CGTGATATTAGCACAT-C
* * * * *
298651 GA---CACCCTGCCTACTCCACACGTTAGAGCACTCGACGTAAGATCAGGTCATCCTGCCTACTC
1 TATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTC
* * * * *
298713 CCCTTTGGAAGCGCTCGGCATGCACTCTGTCT-CCTCTGCCTACTCTAAACGTTGAAGCGCTCGG
66 CCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACC-CTGCCTACTCTACACGTTGAAGTGCTCGA
*
298777 CGTGACATTAAGGCACATC
130 CGTGATATT-A-GCACATC
298796 TTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACT
1 -TATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACT
* * *
298861 CCCCTCTGGAAGCGCTTGGCATGTACTCTGTCTCCCCTGCCTACTCT-CAACGTTGAAGTGCTCG
65 CCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACTCTAC-ACGTTGAAGTGCTCG
298925 ACGTGATATTATAGCACATC
129 ACGTGATA-T-TAGCACATC
*
298945 TTGTTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACT
1 -TATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACT
* *
299010 CCCCTCTGGAAGCGCTCGGCATGTACTCTGTCTCCCCTGCCTACTCT-CAACGTTGAAGTGCTCG
65 CCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACTCTAC-ACGTTGAAGTGCTCG
*
299074 --GTG----T-G-ATAT-
129 ACGTGATATTAGCACATC
** ** * * *
299083 TATAACACCCTACCTACTCCACACGTTAGAGCGCCCGGCGTAAGATCAAGTCATCCTGCCTACTC
1 TATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTC
* * * * * * * * *
299148 CCCACTGAAAGCGCTCGGCATGAACTCTGAC-CCCCTTCCAACTCTTA-ACGGTGAAGCGCTCGG
66 CCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACTC-TACACGTTGAAGTGCTCGA
* * *
299211 CGTGAAAATAG--GA--
130 CGTGATATTAGCACATC
* * * * * *
299224 -A--T-ACCCTGCCTAC-CCTATACATTAGAGCGCCCGGCGTAAGATCAGGTCATCCGGCCTACT
1 TATTTCACCCGGCCTACTCC-ACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACT
*
299284 CCCCACTGGAAGCGCTCGGCATGAACTCTGTC
65 CCCCTCTGGAAGCGCTCGGCATGAACTCTGTC
299316 CCCCTTCCAA
Statistics
Matches: 706, Mismatches: 67, Indels: 76
0.83 0.08 0.09
Matches are distributed among these distances:
136 28 0.04
137 275 0.39
138 6 0.01
139 5 0.01
140 3 0.00
141 2 0.00
142 2 0.00
143 1 0.00
145 1 0.00
146 2 0.00
147 4 0.01
148 2 0.00
149 370 0.52
150 4 0.01
151 1 0.00
ACGTcount: A:0.21, C:0.35, G:0.21, T:0.24
Consensus pattern (146 bp):
TATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTC
CCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACTCTACACGTTGAAGTGCTCGAC
GTGATATTAGCACATC
Found at i:298765 original size:137 final size:137
Alignment explanation
Indices: 298523--299349 Score: 881
Period size: 137 Copynumber: 5.9 Consensus size: 137
298513 TTTCACCCGA
* *
298523 CCTACTCCACACGTTAGGGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTAGAAGC
1 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
* * * *
298588 GCTCGGCATGAACTCTGTCTACCCTCCCTACCCTACACGTTG-AGATGCTCGGCGTGA-ATCTGG
66 GCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAG-TGCTCGGCGTGACAT-TGG
*
298651 GACACCCTG
129 AACACCCTG
* * * *
298660 CCTACTCCACACGTTAGAGCACTCGACGTAAGATCAGGTCATCCTGCCTACTCCCCTTTGGAAGC
1 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
* * *
298725 GCTCGGCATGCACTCTGTCTCCTCTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGACATTAAGG
66 GCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGTGCTCGGCGTGACATT--GG
*
298790 CACATCTTATTTCACCCGG
129 ---A----A---CACCCTG
298809 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
1 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
* * * * *
298874 GCTTGGCATGTACTCTGTCTCCCCTGCCTACTCTCAACGTTGAAGTGCTCGACGTGATATTATAG
66 GCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGTGCTCGGCGTGACA-T-T-G
* *
298939 CACATCTTGTTTCACCCGG
128 GA-A--------CACCCTG
298958 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
1 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
* * * * **
299023 GCTCGGCATGTACTCTGTCTCCCCTGCCTACTCTCAACGTTGAAGTGCTCGGTGTGATATTATAA
66 GCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGTGCTCGGCGTGACATTGGAA
*
299088 CACCCTA
131 CACCCTG
* * * * *
299095 CCTACTCCACACGTTAGAGCGCCCGGCGTAAGATCAAGTCATCCTGCCTACTCCCCACTGAAAGC
1 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
* * * * * * * *
299160 GCTCGGCATGAACTCTGAC-CCCCTTCCAACTCTTAACGGTGAAGCGCTCGGCGTGAAAATAGGA
66 GCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGTGCTCGGCGTG-ACATTGGA
*
299224 ATACCCTG
130 ACACCCTG
* * * * * *
299232 CCTAC-CCTATACATTAGAGCGCCCGGCGTAAGATCAGGTCATCCGGCCTACTCCCCACTGGAAG
1 CCTACTCC-ACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAG
* * * * *
299296 CGCTCGGCATGAACTCTGTC-CCCCTTCCAACTCTTAATGTTGAAGCGCTCGGCG
65 CGCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGTGCTCGGCG
299350 AAATTCCTTA
Statistics
Matches: 605, Mismatches: 62, Indels: 46
0.85 0.09 0.06
Matches are distributed among these distances:
136 32 0.05
137 306 0.51
138 4 0.01
139 2 0.00
144 1 0.00
145 1 0.00
146 2 0.00
147 2 0.00
148 1 0.00
149 250 0.41
150 3 0.00
151 1 0.00
ACGTcount: A:0.21, C:0.35, G:0.21, T:0.24
Consensus pattern (137 bp):
CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
GCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGTGCTCGGCGTGACATTGGAA
CACCCTG
Found at i:298891 original size:286 final size:283
Alignment explanation
Indices: 298373--299349 Score: 1122
Period size: 286 Copynumber: 3.4 Consensus size: 283
298363 ATTTCACCTG
298373 GCCTACTCCACACGTTA-AGGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCTCTGGAA
1 GCCTACTCCACACGTTAGA-GCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCTCTGGAA
* * * * * * *
298437 GCGCTCGGCATGAACTCTGTCTACCCTGCCTACCCCACACGTTGAGGCGCTCGACCTGATATTAA
65 GCGCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGA-ATT-A
*
298502 AGCACATTCTATTTCACCCGACCTACTCCACACGTTAGGGCGCTCGGCGTAAGACCAGGTCATCC
128 AGCACATT-TATTTCACCCGACCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCC
* *
298567 TGCCTACTCCCCTCTAGAAGCGCTCGGCATGAACTCTGTCTACCCTCCCTACCCTACACGTTG-A
192 TGCCTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCCCCTCCCTACCCTACACGTTGAA
*
298631 GATGCTCGGCGTGAATCTGGGACACCCT
257 G-TGCTCGGCGTGAATCTGGAACACCCT
* * *
298659 GCCTACTCCACACGTTAGAGCACTCGACGTAAGATCAGGTCATCCTGCCTACTCCCCTTTGGAAG
1 GCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCTCTGGAAG
* *
298724 CGCTCGGCATGCACTCTGTCTCCTCTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGACATTAAG
66 CGCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGA-ATTAA-
*
298789 GCACATCTTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCT
129 GCACAT-TTATTTCACCCGACCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCT
* * * *
298854 GCCTACTCCCCTCTGGAAGCGCTTGGCATGTACTCTGTCTCCCCTGCCTACTCT-CAACGTTGAA
193 GCCTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCCCCTCCCTACCCTAC-ACGTTGAA
* * * *
298918 GTGCTCGACGTGATATTATAGCACATCTTGTTTCACCCG
257 GTGCTCGGCGTGA-A-TCT-GGA-A--------CACCCT
*
298957 GCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAG
1 GCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCTCTGGAAG
* * *
299022 CGCTCGGCATGTACTCTGTCTCCCCTGCCTACTCTCAACGTTGAAGTGCTC-G-GTG---T--G-
66 CGCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGAATTAAGC
* ** * * * *
299079 ATA-TTATAACACCCTACCTACTCCACACGTTAGAGCGCCCGGCGTAAGATCAAGTCATCCTGCC
131 ACATTTATTTCACCCGACCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCC
* * * * * * * *
299143 TACTCCCCACTGAAAGCGCTCGGCATGAACTCTGAC-CCCCTTCCAACTCTTA-ACGGTGAAGCG
196 TACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCCCCTCCCTAC-CCTACACGTTGAAGTG
** *
299206 CTCGGCGTGAAAATAGGAATACCCT
260 CTCGGCGTGAATCT-GGAACACCCT
* * * * *
299231 GCCTAC-CCTATACATTAGAGCGCCCGGCGTAAGATCAGGTCATCCGGCCTACTCCCCACTGGAA
1 GCCTACTCC-ACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCTCTGGAA
* * * *
299295 GCGCTCGGCATGAACTCTGTC-CCCCTTCCAACTCTTAATGTTGAAGCGCTCGGCG
65 GCGCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGCGCTCGGCG
299350 AAATTCCTTA
Statistics
Matches: 599, Mismatches: 70, Indels: 55
0.83 0.10 0.08
Matches are distributed among these distances:
273 27 0.05
274 80 0.13
275 1 0.00
282 1 0.00
283 5 0.01
284 1 0.00
285 30 0.05
286 324 0.54
287 5 0.01
288 4 0.01
289 2 0.00
290 1 0.00
292 1 0.00
296 3 0.01
297 1 0.00
298 113 0.19
ACGTcount: A:0.21, C:0.35, G:0.21, T:0.24
Consensus pattern (283 bp):
GCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCTCTGGAAG
CGCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGAATTAAGC
ACATTTATTTCACCCGACCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCC
TACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCCCCTCCCTACCCTACACGTTGAAGTGC
TCGGCGTGAATCTGGAACACCCT
Found at i:301069 original size:92 final size:92
Alignment explanation
Indices: 300960--301141 Score: 328
Period size: 92 Copynumber: 2.0 Consensus size: 92
300950 CATTTAAAAT
* *
300960 TTGTTCCATGTTGTGAATGTTCTTGGAATTTTTATTCAGTTGTTTAATTCAAGAAATGAACACAA
1 TTGTTCCATGTTGTGAATGTGCTTGAAATTTTTATTCAGTTGTTTAATTCAAGAAATGAACACAA
*
301025 GTTCTACTTAAACTCATTCTTAAGCAC
66 GCTCTACTTAAACTCATTCTTAAGCAC
*
301052 TTGTTCCATGTTTTGAATGTGCTTGAAATTTTTATTCAGTTGTTTAATTCAAGAAATGAACACAA
1 TTGTTCCATGTTGTGAATGTGCTTGAAATTTTTATTCAGTTGTTTAATTCAAGAAATGAACACAA
301117 GCTCTACTTAAACTCATTCTTAAGC
66 GCTCTACTTAAACTCATTCTTAAGC
301142 TCTGACAAAC
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 86 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (92 bp):
TTGTTCCATGTTGTGAATGTGCTTGAAATTTTTATTCAGTTGTTTAATTCAAGAAATGAACACAA
GCTCTACTTAAACTCATTCTTAAGCAC
Found at i:302395 original size:14 final size:14
Alignment explanation
Indices: 302376--302424 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
302366 AGATTGGGTT
*
302376 GAACATAAACGGAC
1 GAACATAAACGAAC
* *
302390 GAACATGAGCGAAC
1 GAACATAAACGAAC
* *
302404 GAATATAAATGAAC
1 GAACATAAACGAAC
302418 GAACATA
1 GAACATA
302425 GACAAATCTT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.51, C:0.16, G:0.20, T:0.12
Consensus pattern (14 bp):
GAACATAAACGAAC
Found at i:312415 original size:31 final size:30
Alignment explanation
Indices: 312374--312432 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
312364 AATCAAGCTA
* *
312374 ATTTTAAATATAAATTTTATAGAGTTTAATT
1 ATTTAAAATATAAATTTT-TAAAGTTTAATT
**
312405 ATTTAAAATATTTATTTTTAAAGTTTAA
1 ATTTAAAATATAAATTTTTAAAGTTTAA
312433 GAATTATAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 9 0.38
31 15 0.62
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (30 bp):
ATTTAAAATATAAATTTTTAAAGTTTAATT
Found at i:312734 original size:3 final size:3
Alignment explanation
Indices: 312726--312779 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
312716 GCCTTAAACC
312726 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
312774 CAT CAT
1 CAT CAT
312780 ATAGCTAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:314368 original size:2 final size:2
Alignment explanation
Indices: 314361--314394 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
314351 TTCTCTAACC
314361 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
314395 TCTTTTAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:314465 original size:21 final size:20
Alignment explanation
Indices: 314418--314466 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
314408 TAATGTTATT
*
314418 TAATA-TATCAAATATAATA
1 TAATATTATCAAATATAACA
* *
314437 TAAAATTATGAAATATATACA
1 TAATATTATCAAATATA-ACA
314458 TAATATTAT
1 TAATATTAT
314467 ATTTTAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 4 0.17
20 10 0.42
21 10 0.42
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (20 bp):
TAATATTATCAAATATAACA
Found at i:314855 original size:158 final size:156
Alignment explanation
Indices: 314664--315011 Score: 450
Period size: 156 Copynumber: 2.2 Consensus size: 156
314654 TATTTTATTG
* * * * *
314664 TGGTTTATGAGCATGTGGTTCAAATTTGATAAAAGACGGACTTAAAATAAATGATGAATTGAATA
1 TGGTTTATGAGAATGTGGTTCAAATTTGGTAAAAGACGGAATTAAAATAAATAATGAATTGAAAA
* * *
314729 AATAAGGAAAATAT-AAAAGATTAAGGGACTAAATT-GAAAATATTAAAAAATATTATCAAAAAG
66 AATAAAG-AAATATGAAAA-ATTAA-GGACTAAATTGGAAAATA-AAAAAAAAATTAT-AAAAAG
** * *
314792 AAGAA-TTGAAAGTACATATGTATTCTGCGA
126 AAGAAGTTGAAAACACATAGGTATTCTACGA
*
314822 TGGTTTATGAGAATGTGGTTCAAATTTGGTAAAAGACGGAATTAAAATAAATAATTAATTGAAAA
1 TGGTTTATGAGAATGTGGTTCAAATTTGGTAAAAGACGGAATTAAAATAAATAATGAATTGAAAA
* *
314887 AATAAAGAAATATGAAAAATTAAGGACTAAGTTGGAAAATAAAAAAAAAATTATAAAAAGGAGAA
66 AATAAAGAAATATGAAAAATTAAGGACTAAATTGGAAAATAAAAAAAAAATTATAAAAAGAAGAA
* *
314952 GTTGAAAACACGTAGGTATTCTATGA
131 GTTGAAAACACATAGGTATTCTACGA
* * *
314978 TGGTTTATGAGTATATGATTCAAATTTGGTAAAA
1 TGGTTTATGAGAATGTGGTTCAAATTTGGTAAAA
315012 AAAAAGCAGA
Statistics
Matches: 167, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
155 10 0.06
156 70 0.42
157 18 0.11
158 69 0.41
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (156 bp):
TGGTTTATGAGAATGTGGTTCAAATTTGGTAAAAGACGGAATTAAAATAAATAATGAATTGAAAA
AATAAAGAAATATGAAAAATTAAGGACTAAATTGGAAAATAAAAAAAAAATTATAAAAAGAAGAA
GTTGAAAACACATAGGTATTCTACGA
Found at i:315007 original size:156 final size:158
Alignment explanation
Indices: 314649--315011 Score: 459
Period size: 158 Copynumber: 2.3 Consensus size: 158
314639 TTGAAGTTAT
* * * *
314649 ATAGGTATTTTATTG-TGGTTTATGAGCATGTGGTTCAAATTTGATAAAAGACGGACTTAAAATA
1 ATAGGTATTCTA-TGATGGTTTATGAGAATGTGGTTCAAATTTGGTAAAAGACGGAATTAAAATA
* * * *
314713 AATGATGAATTGAATAAATAAGGAAAATATAAAAGATTAAGGGACTAAATTGAAAATATTAAAAA
65 AATAATGAATTGAAAAAATAAAGAAAATATAAAAGATTAAGGGACTAAATTGAAAATATAAAAAA
* **
314778 ATATTATCAAAAAGAAGAATTGAAAGTAC
130 AAATTATCAAAAAGAAGAATTGAAAACAC
* **
314807 ATATGTATTCTGCGATGGTTTATGAGAATGTGGTTCAAATTTGGTAAAAGACGGAATTAAAATAA
1 ATAGGTATTCTATGATGGTTTATGAGAATGTGGTTCAAATTTGGTAAAAGACGGAATTAAAATAA
* *
314872 ATAATTAATTGAAAAAATAAAG-AAATATGAAAA-ATTAA-GGACTAAGTTGGAAAATA-AAAAA
66 ATAATGAATTGAAAAAATAAAGAAAATAT-AAAAGATTAAGGGACTAAATT-GAAAATATAAAAA
*
314933 AAAATTAT-AAAAAGGAGAAGTTGAAAACAC
129 AAAATTATCAAAAAGAAGAA-TTGAAAACAC
* * * *
314963 GTAGGTATTCTATGATGGTTTATGAGTATATGATTCAAATTTGGTAAAA
1 ATAGGTATTCTATGATGGTTTATGAGAATGTGGTTCAAATTTGGTAAAA
315012 AAAAAGCAGA
Statistics
Matches: 177, Mismatches: 24, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
155 10 0.06
156 70 0.40
157 19 0.11
158 78 0.44
ACGTcount: A:0.47, C:0.04, G:0.18, T:0.30
Consensus pattern (158 bp):
ATAGGTATTCTATGATGGTTTATGAGAATGTGGTTCAAATTTGGTAAAAGACGGAATTAAAATAA
ATAATGAATTGAAAAAATAAAGAAAATATAAAAGATTAAGGGACTAAATTGAAAATATAAAAAAA
AATTATCAAAAAGAAGAATTGAAAACAC
Found at i:316713 original size:14 final size:14
Alignment explanation
Indices: 316694--316725 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
316684 CGTTCGTGAA
316694 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
316708 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
316722 CGTT
1 CGTT
316726 TATGTTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.28, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:316742 original size:24 final size:24
Alignment explanation
Indices: 316695--316743 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
316685 GTTCGTGAAC
* *
316695 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGGTTATGTTCATTCAGTTAT
* *
316719 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGGTTATGTTCATTCAGTTAT
316743 G
1 G
316744 ATTAACCCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.12, C:0.12, G:0.22, T:0.53
Consensus pattern (24 bp):
GTTCGGTTATGTTCATTCAGTTAT
Found at i:317784 original size:16 final size:16
Alignment explanation
Indices: 317763--317803 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
317753 GTCTTCAACG
317763 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
317779 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
317795 TTTATGTTC
1 TTTATGTTC
317804 ACGCGCGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.10, C:0.12, G:0.20, T:0.59
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:319082 original size:25 final size:23
Alignment explanation
Indices: 319029--319083 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
319019 TTTTATTCTC
319029 TATTTTTAAATTAAATATTTAAA
1 TATTTTTAAATTAAATATTTAAA
*
319052 TTTTTTTAAAATTAAACTATTT-AA
1 TATTTTT-AAATTAAA-TATTTAAA
319076 TCATTTTT
1 T-ATTTTT
319084 CATCCTCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 6 0.22
24 11 0.41
25 10 0.37
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (23 bp):
TATTTTTAAATTAAATATTTAAA
Found at i:322967 original size:20 final size:21
Alignment explanation
Indices: 322942--322993 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
322932 TTTTCCCAAT
*
322942 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
322962 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
322983 TCGCAATGCGA
1 TCGCAATGCGA
322994 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:323007 original size:20 final size:20
Alignment explanation
Indices: 322982--323089 Score: 110
Period size: 20 Copynumber: 5.3 Consensus size: 20
322972 AATTGGGAAA
322982 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
323002 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
323022 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
323043 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
323063 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
*
323083 TTCGCAA
1 ATCGCAA
323090 CGTGATTTAC
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.03
20 58 0.77
21 13 0.17
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:323090 original size:20 final size:20
Alignment explanation
Indices: 323044--323096 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
323034 TAATACAAAA
*
323044 TCGCAACGAGATACTGACTT
1 TCGCAACGAGATTCTGACTT
*
323064 TCGCAACGCGATTCTGACTT
1 TCGCAACGAGATTCTGACTT
*
323084 TCGCAACGTGATT
1 TCGCAACGAGATT
323097 TACATAGCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (20 bp):
TCGCAACGAGATTCTGACTT
Found at i:323642 original size:20 final size:20
Alignment explanation
Indices: 323614--323680 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 20
323604 TTCGAGAATG
323614 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGCGGAAATA
** *
323634 ACTATCGCAACG-AGAAATA
1 AAAATCGCAACGCGGAAATA
**
323653 AAAATCGCAACGC-GAAACC
1 AAAATCGCAACGCGGAAATA
323672 AAAATCGCA
1 AAAATCGCA
323681 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
19 29 0.74
20 10 0.26
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.10
Consensus pattern (20 bp):
AAAATCGCAACGCGGAAATA
Found at i:323679 original size:38 final size:38
Alignment explanation
Indices: 323606--323680 Score: 91
Period size: 39 Copynumber: 2.0 Consensus size: 38
323596 AGAATAGTTT
* * *
323606 CGAGAATGAAAATCGCAACGCGGAAATAACTATCGCAA
1 CGAGAATAAAAATCGCAACGCGGAAACAACAATCGCAA
323644 CGAGAAATAAAAATCGCAACGC-GAAACCAA-AATCGCA
1 CGAG-AATAAAAATCGCAACGCGGAAA-CAACAATCGCA
323681 TTGCGATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 14 0.44
39 18 0.56
ACGTcount: A:0.48, C:0.23, G:0.19, T:0.11
Consensus pattern (38 bp):
CGAGAATAAAAATCGCAACGCGGAAACAACAATCGCAA
Found at i:323698 original size:19 final size:19
Alignment explanation
Indices: 323676--323821 Score: 114
Period size: 19 Copynumber: 8.1 Consensus size: 19
323666 GAAACCAAAA
*
323676 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
323695 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
323714 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
323728 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
323747 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
323761 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
323780 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
323800 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
323820 TC
1 TC
323822 AACCAAAAGA
Statistics
Matches: 101, Mismatches: 14, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
14 19 0.19
16 4 0.04
17 5 0.05
19 41 0.41
20 31 0.31
21 1 0.01
ACGTcount: A:0.12, C:0.25, G:0.21, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:323746 original size:33 final size:33
Alignment explanation
Indices: 323709--323796 Score: 158
Period size: 33 Copynumber: 2.6 Consensus size: 33
323699 GTTGCGATTT
323709 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
323742 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
323775 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
323797 ATTATCTCGT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 38 0.72
34 15 0.28
ACGTcount: A:0.11, C:0.27, G:0.23, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:325712 original size:30 final size:30
Alignment explanation
Indices: 325676--325764 Score: 81
Period size: 30 Copynumber: 3.3 Consensus size: 30
325666 TTGTCTTTGT
325676 TTTGTCTTTTGGTTGAAAGTTTGAAATATA
1 TTTGTCTTTTGGTTGAAAGTTTGAAATATA
***
325706 TTTGTC-TTT-GTT--TTCTTTG-----T-
1 TTTGTCTTTTGGTTGAAAGTTTGAAATATA
325726 TTTGTCTTTTGGTTGAAAGTTTGAAATATA
1 TTTGTCTTTTGGTTGAAAGTTTGAAATATA
325756 TTTGTCTTT
1 TTTGTCTTT
325765 GTTTTCACTG
Statistics
Matches: 43, Mismatches: 6, Indels: 20
0.62 0.09 0.29
Matches are distributed among these distances:
20 6 0.14
21 4 0.09
22 3 0.07
24 4 0.09
26 4 0.09
28 3 0.07
29 4 0.09
30 15 0.35
ACGTcount: A:0.18, C:0.06, G:0.18, T:0.58
Consensus pattern (30 bp):
TTTGTCTTTTGGTTGAAAGTTTGAAATATA
Found at i:325737 original size:50 final size:50
Alignment explanation
Indices: 325669--325770 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
325659 TTAGTATTTG
325669 TCTTTGTTTTGTCTTTTGGTTGAAAGTTTGAAATATATTTGTCTTTGTTT
1 TCTTTGTTTTGTCTTTTGGTTGAAAGTTTGAAATATATTTGTCTTTGTTT
325719 TCTTTGTTTTGTCTTTTGGTTGAAAGTTTGAAATATATTTGTCTTTGTTT
1 TCTTTGTTTTGTCTTTTGGTTGAAAGTTTGAAATATATTTGTCTTTGTTT
325769 TC
1 TC
325771 ACTGTTTAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.16, C:0.07, G:0.18, T:0.60
Consensus pattern (50 bp):
TCTTTGTTTTGTCTTTTGGTTGAAAGTTTGAAATATATTTGTCTTTGTTT
Found at i:326040 original size:21 final size:21
Alignment explanation
Indices: 326016--326085 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
326006 TCATTCCTCG
326016 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
326037 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
326058 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
326079 AGAGTCC
1 AGAGTCC
326086 GATTCACATG
Statistics
Matches: 34, Mismatches: 13, Indels: 4
0.67 0.25 0.08
Matches are distributed among these distances:
20 2 0.06
21 31 0.91
22 1 0.03
ACGTcount: A:0.23, C:0.37, G:0.20, T:0.20
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:326040 original size:42 final size:42
Alignment explanation
Indices: 325964--326082 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
325954 GACTCGCCTG
* * * * * * *
325964 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
326006 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
326048 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
326083 TCCGATTCAC
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:327449 original size:14 final size:14
Alignment explanation
Indices: 327430--327465 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
327420 ATTGTTTAAT
327430 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
327444 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
327458 TGATTTGT
1 TGATTTGT
327466 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:327613 original size:14 final size:14
Alignment explanation
Indices: 327590--327646 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
327580 GCGAAATGAA
*
327590 AATCGTAACGAGAG
1 AATCGCAACGAGAG
*
327604 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
327623 AATCGCAACGAGAG
1 AATCGCAACGAGAG
327637 AATCGCAACG
1 AATCGCAACG
327647 CGAAATTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:327617 original size:33 final size:33
Alignment explanation
Indices: 327572--327661 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
327562 AAAAAGTACT
* *
327572 ATCGCAATGCGAAATGAAAATCGTAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
327605 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
327638 ATCGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
327662 GTTGCGATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:327628 original size:19 final size:19
Alignment explanation
Indices: 327572--327632 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
327562 AAAAAGTACT
*
327572 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
* *
327591 ATCGTAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
327605 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
327624 ATCGCAACG
1 ATCGCAACG
327633 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
14 9 0.27
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 18 0.55
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:327679 original size:19 final size:19
Alignment explanation
Indices: 327657--327807 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
327647 CGAAATTAAA
327657 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
327676 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
327691 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* * *
327709 TTTGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
327723 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
327742 TTCGCATTGCGATTCTC--
1 TTCGCGTTGCGATTTTCAT
327759 TT---GTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
327775 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
327794 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
327808 AGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 29 0.31
16 5 0.05
17 5 0.05
19 46 0.48
20 10 0.11
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.43
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:327703 original size:33 final size:32
Alignment explanation
Indices: 327661--327787 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
327651 ATTAAATTCG
327661 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* *
327694 CGTTGCGATTTTCATTTTGCATTGCGAAATT-CG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
327727 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
327760 TGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
327788 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:327732 original size:66 final size:66
Alignment explanation
Indices: 327654--327786 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
327644 ACGCGAAATT
*
327654 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTTGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
327719 G
66 G
* *
327720 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTTGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
327785 G
66 G
327786 A
1 A
327787 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.43
Consensus pattern (66 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:330030 original size:12 final size:12
Alignment explanation
Indices: 330013--330037 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
330003 TCTTCGGGGA
330013 CTTTTTCTTCTT
1 CTTTTTCTTCTT
330025 CTTTTTCTTCTT
1 CTTTTTCTTCTT
330037 C
1 C
330038 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:331031 original size:20 final size:20
Alignment explanation
Indices: 331003--331075 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
330993 GATTATGTAT
*
331003 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
331023 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
331043 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
331063 TATCGCATTGCGA
1 TATCGCGTTGCGA
331076 TTTTACCAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:331107 original size:20 final size:21
Alignment explanation
Indices: 331065--331116 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
331055 ATAGTCAGTA
331065 TCGCATTGCGATTTTACCAAT
1 TCGCATTGCGATTTTACCAAT
* **
331086 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
331106 TCGCATTGCGA
1 TCGCATTGCGA
331117 ATTGGGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACCAAT
Found at i:333330 original size:21 final size:22
Alignment explanation
Indices: 333299--333339 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
333289 TTAAAAATTA
333299 TAAAGGTAGTA-CTGATACTCAT
1 TAAAGGTAGTATC-GATACTCAT
333321 TAAA-GTAGTATCGATACTC
1 TAAAGGTAGTATCGATACTC
333340 TCTGTCCTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.32
Consensus pattern (22 bp):
TAAAGGTAGTATCGATACTCAT
Found at i:333875 original size:49 final size:49
Alignment explanation
Indices: 333727--334029 Score: 355
Period size: 49 Copynumber: 6.2 Consensus size: 49
333717 TCTATGATGA
* **
333727 AAGTTAAATGCAAAATGGTGCATTTTTTTGCAGAAAATTGCCACTAATGC
1 AAGTTAAATGCAAAATGGTGCA-TTTTTGGCAGAAAGGTGCCACTAATGC
* * *
333777 AAGTGAAATGCATAACT-GTGCATTTTT-GCAGAAAGGTGCCACTATTGC
1 AAGTTAAATGCA-AAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGC
*
333825 AAGTTAAATGCAAAATGGTGTATTTTTGGCAGAAAGGTGCCACTAATGC
1 AAGTTAAATGCAAAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGC
* * *
333874 AAGTTAAATGCAAAATAGTGTATTTTTGGCAGAAATGTGCCACTAATGC
1 AAGTTAAATGCAAAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGC
* * * *
333923 AAGTGAAATGCATAATTGTGCATTTTTGGCAGAAATGTGCCACTAATGC
1 AAGTTAAATGCAAAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGC
* * * * * *
333972 AAGTTAAATGTC-TAACGGTGCA-TTTTGGCATAAAAGTACCATTAATG-
1 AAGTTAAATG-CAAAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGC
334019 ACAGTTAAATG
1 A-AGTTAAATG
334030 GGTAATAGTG
Statistics
Matches: 226, Mismatches: 22, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
47 4 0.02
48 68 0.30
49 134 0.59
50 17 0.08
51 3 0.01
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (49 bp):
AAGTTAAATGCAAAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGC
Found at i:334039 original size:146 final size:146
Alignment explanation
Indices: 333727--334029 Score: 416
Period size: 146 Copynumber: 2.1 Consensus size: 146
333717 TCTATGATGA
* * *
333727 AAGTTAAATGCAAAATGGTGCATTTTTTTGCAGAAAATTGCCACTAATGCAAGTGAAATGCATAA
1 AAGTTAAATGCAAAATAGTGTA-TTTTTGGCAGAAAATTGCCACTAATGCAAGTGAAATGCATAA
* * *
333792 CTGTGCATTTTTGCAGAAAGGTGCCACTATTGCAAGTTAAATGCAAAATGGTGTATTTTTGGCAG
65 CTGTGCATTTTTGCAGAAAGGTGCCACTAATGCAAGTTAAATGCAAAACGGTGCATTTTTGGCAG
* *
333857 AAAGGTGCCACTAATGC
130 AAAAGTACCACTAATGC
333874 AAGTTAAATGCAAAATAGTGTATTTTTGGCAG-AAATGTGCCACTAATGCAAGTGAAATGCATAA
1 AAGTTAAATGCAAAATAGTGTATTTTTGGCAGAAAAT-TGCCACTAATGCAAGTGAAATGCATAA
* * *
333938 TTGTGCATTTTTGGCAGAAATGTGCCACTAATGCAAGTTAAATGTC-TAACGGTGCA-TTTTGGC
65 CTGTGCATTTTT-GCAGAAAGGTGCCACTAATGCAAGTTAAATG-CAAAACGGTGCATTTTTGGC
* *
334001 ATAAAAGTACCATTAATG-
128 AGAAAAGTACCACTAATGC
334019 ACAGTTAAATG
1 A-AGTTAAATG
334030 GGTAATAGTG
Statistics
Matches: 139, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
145 5 0.04
146 77 0.55
147 56 0.40
148 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (146 bp):
AAGTTAAATGCAAAATAGTGTATTTTTGGCAGAAAATTGCCACTAATGCAAGTGAAATGCATAAC
TGTGCATTTTTGCAGAAAGGTGCCACTAATGCAAGTTAAATGCAAAACGGTGCATTTTTGGCAGA
AAAGTACCACTAATGC
Found at i:334698 original size:10 final size:11
Alignment explanation
Indices: 334675--334731 Score: 57
Period size: 12 Copynumber: 5.3 Consensus size: 11
334665 GTCCGCTTAA
334675 ATTA-ATAT-T
1 ATTATATATAT
334684 ATTATATA-AT
1 ATTATATATAT
*
334694 ATTATAAATTAT
1 ATTATATA-TAT
*
334706 AATATATATAT
1 ATTATATATAT
334717 ATATATATATAT
1 AT-TATATATAT
334729 ATT
1 ATT
334732 TACATTTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 4 0.10
10 11 0.28
11 5 0.13
12 19 0.49
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
ATTATATATAT
Found at i:334710 original size:20 final size:22
Alignment explanation
Indices: 334681--334721 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
334671 TTAAATTAAT
*
334681 ATTATTATATA-ATAT-TATAA
1 ATTATAATATATATATATATAA
334701 ATTATAATATATATATATATA
1 ATTATAATATATATATATATA
334722 TATATATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 4 0.22
22 4 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTATAATATATATATATATAA
Found at i:334714 original size:2 final size:2
Alignment explanation
Indices: 334686--334730 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
334676 TTAATATTAT
*
334686 TA TA TA -A TA T- TA TA AA T- TA TA -A 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
334724 TA TA TA T
1 TA TA TA T
334731 TTACATTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
1 4 0.11
2 33 0.89
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:335841 original size:4 final size:4
Alignment explanation
Indices: 335825--335970 Score: 96
Period size: 4 Copynumber: 38.0 Consensus size: 4
335815 ATCCTTATTA
* * * * * *
335825 TTAT TTCT TTAT TTAT TTAT TCAT CTAAT TTA- ATAT TT-T ATAT CTA-
1 TTAT TTAT TTAT TTAT TTAT TTAT -TTAT TTAT TTAT TTAT TTAT TTAT
*
335871 TTA- TTA- TTA- TTAT TTAT TTAT TTAT TTAT TTAT CTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * *
335916 TTAT CTAT TTAT TTA- TT-T TTATT TTAT TT-T ATTAC TTATT TTTT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTA-T TTAT TTAT -TTAT TTA-T TTAT TTAT
335964 TT-T TTAT
1 TTAT TTAT
335971 ACATTATTAT
Statistics
Matches: 113, Mismatches: 18, Indels: 22
0.74 0.12 0.14
Matches are distributed among these distances:
3 23 0.20
4 81 0.72
5 9 0.08
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:336216 original size:2 final size:2
Alignment explanation
Indices: 336211--336241 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
336201 TTTTTTTCTG
336211 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
336242 TTTTATTTTT
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:336379 original size:3 final size:3
Alignment explanation
Indices: 336371--336402 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
336361 TAATTTCCTC
*
336371 ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
336403 AGGCTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:340433 original size:99 final size:98
Alignment explanation
Indices: 340317--340519 Score: 284
Period size: 99 Copynumber: 2.1 Consensus size: 98
340307 ATTATAATAT
* *
340317 TATATATATACAATAAAGCATGAGTTGTCCCTCT-AGAGCAATTGGTTAAACGCCCCGGCTCTAT
1 TATATTTATACAATAAAGCATGAGCTGTCCCTCTAAG-GCAATTGGTTAAACGCCCCGGCTCTAT
*
340381 GGATAAGATTTAG-CAAGCCTGATAAAGGTGATTA
65 GGATAAGATTCAGTCAA-CCTGATAAAGGTGATTA
* * * *
340415 TAATATTTATACAATAAAGCTTGAGCTGTCCCTCTAAGGTAATTGGTTAAACGCCCTGGCTTTAT
1 T-ATATTTATACAATAAAGCATGAGCTGTCCCTCTAAGGCAATTGGTTAAACGCCCCGGCTCTAT
* *
340480 GGATAAGATTCAGTTAACCTGATAAAGGTGTTTA
65 GGATAAGATTCAGTCAACCTGATAAAGGTGATTA
340514 TATATT
1 TATATT
340520 GAACTGTCCC
Statistics
Matches: 93, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
98 6 0.06
99 83 0.89
100 4 0.04
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (98 bp):
TATATTTATACAATAAAGCATGAGCTGTCCCTCTAAGGCAATTGGTTAAACGCCCCGGCTCTATG
GATAAGATTCAGTCAACCTGATAAAGGTGATTA
Found at i:342327 original size:60 final size:62
Alignment explanation
Indices: 342172--342333 Score: 177
Period size: 65 Copynumber: 2.6 Consensus size: 62
342162 GCTCGAGATT
* * * * *
342172 GGATTTCAAGTTCACAACGAATGATATCCAACTCAAAGCCAATTTGGAGAAACTTACTCAAGATT
1 GGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATTTGGAGAAACTAACTC---ATC
* * *
342237 GGATTTCAACTTCACGACGAAGGATTTCCAACTCAAAACCAATTTGGTA-AAAC-AATTC-TC
1 GGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATTTGG-AGAAACTAACTCATC
* *
342297 GGATTTCAACTTCAAAACGAAGGATATCCAATTCAAA
1 GGATTTCAACTTCACAACGAAGGATATCCAACTCAAA
342334 GATCAACTTC
Statistics
Matches: 84, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
60 34 0.40
64 3 0.04
65 46 0.55
66 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.26
Consensus pattern (62 bp):
GGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATTTGGAGAAACTAACTCATC
Found at i:342617 original size:85 final size:85
Alignment explanation
Indices: 342469--342820 Score: 431
Period size: 85 Copynumber: 4.1 Consensus size: 85
342459 CCCAGTGCAA
** * ** *
342469 CATAACTCAATACGAGAAGGGTTATCTGTCATCAAAGACCTTTGAGTTTGATTACATTCAGCTCA
1 CATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTTGAGTCCGATTACACTCAGCTCA
*
342534 AAGGCATGTCAAATTTATAG
66 AAGGCATATCAAATTTATAG
* * *
342554 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAG-GCTTTCGAGTCCGATTACACTCAGCTC
1 CATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTT-GAGTCCGATTACACTCAGCTC
*
342618 AAAGGCACATCAAATTTATAG
65 AAAGGCATATCAAATTTATAG
* * * *
342639 CATAACTCAAGGCGAGAAAGGTTATTTGTCAACAAAGACCTTCGAG-CTCGATTACACTAAGCTC
1 CATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTTGAGTC-CGATTACACTCAGCTC
* *
342703 AAATGCAT-GCAAAATTTATAG
65 AAAGGCATATC-AAATTTATAG
* * * *
342724 TATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTTGAGTTCGATTACATTCAGCTCA
1 CATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTTGAGTCCGATTACACTCAGCTCA
* * * *
342789 GAGGTAAATCAAATTTACAG
66 AAGGCATATCAAATTTATAG
342809 CATAACTCAAGG
1 CATAACTCAAGG
342821 TAATAAGGTC
Statistics
Matches: 225, Mismatches: 36, Indels: 12
0.82 0.13 0.04
Matches are distributed among these distances:
84 6 0.03
85 215 0.96
86 4 0.02
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (85 bp):
CATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTTGAGTCCGATTACACTCAGCTCA
AAGGCATATCAAATTTATAG
Found at i:343447 original size:10 final size:11
Alignment explanation
Indices: 343424--343490 Score: 70
Period size: 12 Copynumber: 6.3 Consensus size: 11
343414 GTCCACTTAA
343424 ATTA-ATAT-T
1 ATTATATATAT
343433 ATTATATA-AT
1 ATTATATATAT
*
343443 ATTATAAAT-T
1 ATTATATATAT
*
343453 ATAATATATAT
1 ATTATATATAT
343464 ATATATATATAT
1 AT-TATATATAT
343476 ATATATATATAT
1 AT-TATATATAT
343488 ATT
1 ATT
343491 TCCATTTTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
9 4 0.08
10 19 0.39
11 4 0.08
12 22 0.45
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
ATTATATATAT
Found at i:343463 original size:2 final size:2
Alignment explanation
Indices: 343435--343489 Score: 73
Period size: 2 Copynumber: 29.5 Consensus size: 2
343425 TTAATATTAT
*
343435 TA TA TA -A TA T- TA TA AA T- TA TA -A 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
343473 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
343490 TTCCATTTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
1 4 0.09
2 43 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:344595 original size:4 final size:4
Alignment explanation
Indices: 344579--344704 Score: 74
Period size: 4 Copynumber: 33.5 Consensus size: 4
344569 ATCCTTATTA
* * * * * *
344579 TTAT TTCT TTAT TTAT TTAT TCAT CTAAT TTA- ATAT TT-T ATAT CTA-
1 TTAT TTAT TTAT TTAT TTAT TTAT -TTAT TTAT TTAT TTAT TTAT TTAT
*
344625 TTA- TTA- TTA- TTAT TTAT TTAT CTAT TTAT TTA- TT-T TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * *
344668 TTAT CTAT TTAT TT-T ATTAC TTA- TTAT TTTT TTAT TT
1 TTAT TTAT TTAT TTAT -TTAT TTAT TTAT TTAT TTAT TT
344705 TGTTTATACA
Statistics
Matches: 96, Mismatches: 17, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
3 23 0.24
4 70 0.73
5 3 0.03
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:344653 original size:34 final size:33
Alignment explanation
Indices: 344615--344763 Score: 104
Period size: 30 Copynumber: 4.7 Consensus size: 33
344605 AATTTAATAT
344615 TTTATATCTATTATTATTATTATTTATTTATCTA
1 TTTATAT-TATTATTATTATTATTTATTTATCTA
* * *
344649 TTTAT-TTATTTTTA-T-TTATTTATCTATTTA
1 TTTATATTATTATTATTATTATTTATTTATCTA
*
344679 TTT-TATTACTTATTATT-TT-TTTA-TT-T-TG
1 TTTATATTA-TTATTATTATTATTTATTTATCTA
* * *
344707 TTTATA-CATTATTATATATATATATATTTTTCT-
1 TTTATATTATTATTAT-TAT-TATTTATTTATCTA
* *
344740 TTTTTATTATTACTATTATTATTT
1 TTTATATTATTATTATTATTATTT
344764 TCTTTTTATT
Statistics
Matches: 91, Mismatches: 12, Indels: 26
0.71 0.09 0.20
Matches are distributed among these distances:
27 7 0.08
28 6 0.07
29 5 0.05
30 21 0.23
31 13 0.14
32 16 0.18
33 10 0.11
34 13 0.14
ACGTcount: A:0.26, C:0.05, G:0.01, T:0.68
Consensus pattern (33 bp):
TTTATATTATTATTATTATTATTTATTTATCTA
Found at i:344657 original size:26 final size:26
Alignment explanation
Indices: 344573--344696 Score: 112
Period size: 26 Copynumber: 4.6 Consensus size: 26
344563 AGTTCAATCC
* *
344573 TTATTATTATTTCTTTATTTATTTAT
1 TTATTATTATTTATTTATCTATTTAT
*
344599 TCATCTAATTTAATATT-TTATATCTA-TTA-
1 TTAT-T-A-TT-AT-TTATT-TATCTATTTAT
344628 TTATTATTATTTATTTATCTATTTAT
1 TTATTATTATTTATTTATCTATTTAT
*
344654 TTATTTTTATTTATTTATCTATTTATT
1 TTATTATTATTTATTTATCTATTTA-T
344681 TTATTACTTA-TTATTT
1 TTATTA-TTATTTATTT
344697 TTTTATTTTG
Statistics
Matches: 82, Mismatches: 5, Indels: 21
0.76 0.05 0.19
Matches are distributed among these distances:
24 8 0.10
25 7 0.09
26 29 0.35
27 14 0.17
28 5 0.06
29 5 0.06
30 7 0.09
31 7 0.09
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.68
Consensus pattern (26 bp):
TTATTATTATTTATTTATCTATTTAT
Found at i:344659 original size:43 final size:45
Alignment explanation
Indices: 344586--344705 Score: 115
Period size: 43 Copynumber: 2.7 Consensus size: 45
344576 TTATTATTTC
* *
344586 TTTATTTATTTATTCATCTAATTTA-ATATTTTATATCTA-TTAT-TA
1 TTTA-TTATTTATTTATCT-ATTTATTTATTTT-TATCTATTTATCTA
*
344631 -TTATTATTTATTTATCTATTTATTTATTTTTATTTATTTATCTA
1 TTTATTATTTATTTATCTATTTATTTATTTTTATCTATTTATCTA
* * *
344675 TTTATTTTATTACTTAT-TATTTTTTTATTTT
1 TTTATTAT-TTATTTATCTATTTATTTATTTT
344706 GTTTATACAT
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
42 10 0.16
43 23 0.36
44 5 0.08
45 19 0.30
46 7 0.11
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (45 bp):
TTTATTATTTATTTATCTATTTATTTATTTTTATCTATTTATCTA
Found at i:345047 original size:14 final size:13
Alignment explanation
Indices: 345010--345036 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
345000 TGTTTATTCC
345010 TATTTGTTTTATT
1 TATTTGTTTTATT
345023 TATTTGTTTTATT
1 TATTTGTTTTATT
345036 T
1 T
345037 TAGTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (13 bp):
TATTTGTTTTATT
Found at i:346175 original size:34 final size:31
Alignment explanation
Indices: 346098--346211 Score: 133
Period size: 30 Copynumber: 3.6 Consensus size: 31
346088 TAATCGGATT
*
346098 AGCACTATAGTGTGTAAGGGCACTTAGTGC-
1 AGCACTATAGTGTGTAAGGACACTTAGTGCA
*
346128 AGCACTATGGTGTGTAAGGACACTTAGTGCA
1 AGCACTATAGTGTGTAAGGACACTTAGTGCA
* *
346159 TATGGTACTATAGTGTGTAAGGACACTTAATGCA
1 -A--GCACTATAGTGTGTAAGGACACTTAGTGCA
* *
346193 A-CACTGTGGTGTGTAAGGA
1 AGCACTATAGTGTGTAAGGA
346212 AGCTCAGTGC
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
30 43 0.60
32 1 0.01
33 1 0.01
34 27 0.38
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (31 bp):
AGCACTATAGTGTGTAAGGACACTTAGTGCA
Found at i:346203 original size:64 final size:64
Alignment explanation
Indices: 346101--346229 Score: 197
Period size: 64 Copynumber: 2.0 Consensus size: 64
346091 TCGGATTAGC
* * * *
346101 ACTATAGTGTGTAAGGGCACTTAGTGCAGCACTATGGTGTGTAAGGACA-CTTAGTGCATATGGT
1 ACTATAGTGTGTAAGGACACTTAATGCAACACTATGGTGTGTAAGGA-AGCTCAGTGCATATGGT
*
346165 ACTATAGTGTGTAAGGACACTTAATGCAACACTGTGGTGTGTAAGGAAGCTCAGTGCATATGGT
1 ACTATAGTGTGTAAGGACACTTAATGCAACACTATGGTGTGTAAGGAAGCTCAGTGCATATGGT
346229 A
1 A
346230 AGCACTTTGG
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
63 1 0.02
64 58 0.98
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (64 bp):
ACTATAGTGTGTAAGGACACTTAATGCAACACTATGGTGTGTAAGGAAGCTCAGTGCATATGGT
Found at i:354576 original size:31 final size:31
Alignment explanation
Indices: 354541--354616 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
354531 TCAAAAACAA
*
354541 TAAGATATGGTCATTTTTGTTTTCATTTAAT
1 TAAGATATGGTCATTTTCGTTTTCATTTAAT
* *
354572 TAAGATATGGTCACTTTCGTTTTTATTTAAT
1 TAAGATATGGTCATTTTCGTTTTCATTTAAT
*
354603 TAAAATATGGTCAT
1 TAAGATATGGTCAT
354617 CCCGAATTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.29, C:0.08, G:0.13, T:0.50
Consensus pattern (31 bp):
TAAGATATGGTCATTTTCGTTTTCATTTAAT
Found at i:355314 original size:20 final size:21
Alignment explanation
Indices: 355280--355319 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
355270 AAATTTTTTA
* *
355280 AAAAATAATATAATT-TGAAG
1 AAAAATAAAAAAATTATGAAG
355300 AAAAATAAAAAAATTATGAA
1 AAAAATAAAAAAATTATGAA
355320 CCGGATACTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (21 bp):
AAAAATAAAAAAATTATGAAG
Found at i:358294 original size:24 final size:24
Alignment explanation
Indices: 358267--358312 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
358257 TCATATAAAT
*
358267 TGCACCGAAGTGCCGCGTAGAATA
1 TGCACCGAAGTGCCACGTAGAATA
** *
358291 TGCATTGAAGTGTCACGTAGAA
1 TGCACCGAAGTGCCACGTAGAA
358313 ATGTCCCGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (24 bp):
TGCACCGAAGTGCCACGTAGAATA
Found at i:358334 original size:23 final size:23
Alignment explanation
Indices: 358308--358387 Score: 115
Period size: 23 Copynumber: 3.5 Consensus size: 23
358298 AAGTGTCACG
358308 TAGAAATGTCCCGAAGGACCACA
1 TAGAAATGTCCCGAAGGACCACA
* *
358331 TAGATATGTCCCGAAGGACCGCA
1 TAGAAATGTCCCGAAGGACCACA
* *
358354 TAGAAATGTCACGAAGGACCACG
1 TAGAAATGTCCCGAAGGACCACA
*
358377 TAGAATTGTCC
1 TAGAAATGTCC
358388 TTTAGGACCG
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (23 bp):
TAGAAATGTCCCGAAGGACCACA
Done.