Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006457.1 Corchorus capsularis cultivar CVL-1 contig06478, 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: 76420
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1487 original size:20 final size:20
Alignment explanation
Indices: 1462--1502 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
1452 CAAAGCTACT
1462 ACCC-AAAGCCCCAAGTTTAA
1 ACCCAAAAG-CCCAAGTTTAA
1482 ACCCAAAAGCCCAAGTTTAA
1 ACCCAAAAGCCCAAGTTTAA
1502 A
1 A
1503 GCCCGAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.44, C:0.32, G:0.10, T:0.15
Consensus pattern (20 bp):
ACCCAAAAGCCCAAGTTTAA
Found at i:3990 original size:16 final size:17
Alignment explanation
Indices: 3969--4002 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3959 AAAACATGGG
3969 ATATTTACCAAG-CCAA
1 ATATTTACCAAGTCCAA
*
3985 ATATTTGCCAAGTCCAA
1 ATATTTACCAAGTCCAA
4002 A
1 A
4003 GTAGTTCTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.24, G:0.09, T:0.26
Consensus pattern (17 bp):
ATATTTACCAAGTCCAA
Found at i:5782 original size:10 final size:10
Alignment explanation
Indices: 5767--5791 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5757 GAGGACTCTA
5767 GAATTTTCTG
1 GAATTTTCTG
5777 GAATTTTCTG
1 GAATTTTCTG
5787 GAATT
1 GAATT
5792 GAGCAGAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:11596 original size:35 final size:35
Alignment explanation
Indices: 11544--11621 Score: 120
Period size: 35 Copynumber: 2.2 Consensus size: 35
11534 TTTTAAATCG
* * *
11544 CAAAATCTTTTTTTTTTAGAAAAATCGGAAAAAAG
1 CAAAAACTTTTTTTTTTAGAAAAAACGGAAAAAAA
*
11579 GAAAAACTTTTTTTTTTAGAAAAAACGGAAAAAAA
1 CAAAAACTTTTTTTTTTAGAAAAAACGGAAAAAAA
11614 CAAAAACT
1 CAAAAACT
11622 AATTCTTGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.29
Consensus pattern (35 bp):
CAAAAACTTTTTTTTTTAGAAAAAACGGAAAAAAA
Found at i:14762 original size:2 final size:2
Alignment explanation
Indices: 14738--14800 Score: 58
Period size: 2 Copynumber: 32.5 Consensus size: 2
14728 TTTATGGCTT
* * * * *
14738 TC TC TC AC TC AC TC AC TC AC TC TC TC TC TC TC TC -C CC TC -C
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
14778 TC TC TC TC TC TC TC TC TT TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC T
14801 TCCTTTGATA
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
1 2 0.04
2 46 0.96
ACGTcount: A:0.06, C:0.51, G:0.00, T:0.43
Consensus pattern (2 bp):
TC
Found at i:20239 original size:19 final size:19
Alignment explanation
Indices: 20215--20255 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
20205 TTGGCTCCTC
*
20215 ATTTTTGCTTCCAATTGCA
1 ATTTTTGCTACCAATTGCA
*
20234 ATTTTTGCTACCAATTTCA
1 ATTTTTGCTACCAATTGCA
20253 ATT
1 ATT
20256 CCAACTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.24, C:0.20, G:0.07, T:0.49
Consensus pattern (19 bp):
ATTTTTGCTACCAATTGCA
Found at i:25543 original size:11 final size:10
Alignment explanation
Indices: 25527--25551 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
25517 AAGTAACTTG
25527 AAAAAAAAAT
1 AAAAAAAAAT
25537 AAAAAAAAAT
1 AAAAAAAAAT
25547 AAAAA
1 AAAAA
25552 GTAAGGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAAAAAT
Found at i:40648 original size:10 final size:10
Alignment explanation
Indices: 40633--40658 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
40623 AGTTGCTGCC
40633 AAATTCCAGA
1 AAATTCCAGA
40643 AAATTCCAGA
1 AAATTCCAGA
40653 AAATTC
1 AAATTC
40659 TAGAGTCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (10 bp):
AAATTCCAGA
Found at i:41607 original size:6 final size:6
Alignment explanation
Indices: 41596--41622 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
41586 ATTAATCTGC
41596 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
41623 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:47178 original size:20 final size:21
Alignment explanation
Indices: 47129--47179 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
47119 CAAATTATGC
47129 ATGTTTTTATAGCTATTTTTAT
1 ATGTTTTT-TAGCTATTTTTAT
**
47151 ATACTTTTT-GCTATTTTTAT
1 ATGTTTTTTAGCTATTTTTAT
47171 ATGTTTTTT
1 ATGTTTTTT
47180 TACCCTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 18 0.72
21 1 0.04
22 6 0.24
ACGTcount: A:0.20, C:0.06, G:0.08, T:0.67
Consensus pattern (21 bp):
ATGTTTTTTAGCTATTTTTAT
Found at i:47777 original size:10 final size:10
Alignment explanation
Indices: 47762--47787 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
47752 AGTTGCTGCC
47762 AAATTCCAGA
1 AAATTCCAGA
47772 AAATTCCAGA
1 AAATTCCAGA
47782 AAATTC
1 AAATTC
47788 TAGAGTCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (10 bp):
AAATTCCAGA
Found at i:48738 original size:6 final size:6
Alignment explanation
Indices: 48727--48753 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
48717 ATTAATCTGC
48727 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
48754 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:52723 original size:35 final size:35
Alignment explanation
Indices: 52684--52770 Score: 111
Period size: 35 Copynumber: 2.5 Consensus size: 35
52674 ATTAAGTGAA
52684 TCGGTGTAATTAAGTAATTTAATAATCAACTTAAT
1 TCGGTGTAATTAAGTAATTTAATAATCAACTTAAT
** ** *
52719 TCGGTGTAATTAAGTCCTTTGGTGATCAACTTAAT
1 TCGGTGTAATTAAGTAATTTAATAATCAACTTAAT
* *
52754 TCGGTGCAATTGAGTAA
1 TCGGTGTAATTAAGTAA
52771 ATCAGTAAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.38
Consensus pattern (35 bp):
TCGGTGTAATTAAGTAATTTAATAATCAACTTAAT
Found at i:52796 original size:22 final size:21
Alignment explanation
Indices: 52770--53238 Score: 209
Period size: 22 Copynumber: 21.5 Consensus size: 21
52760 CAATTGAGTA
52770 AATCAGTAAAAAGTAAAATGGT
1 AATCAGTAAAAAGTAAAA-GGT
* * *
52792 AATCAGAAAAAAAGAAAAAAG-
1 AATCAG-TAAAAAGTAAAAGGT
** * *
52813 AAGAAG-AAGAAAGTAGAAGAT
1 AATCAGTAA-AAAGTAAAAGGT
** *
52834 AATCAGTAAAGGGCAAAATGGT
1 AATCAGTAAAAAGTAAAA-GGT
* *
52856 AACCAGTAAAAAGTAAAAGAAT
1 AATCAGTAAAAAGTAAAAG-GT
* * * *
52878 AATTAGTAAAGAGTAGAAGAT
1 AATCAGTAAAAAGTAAAAGGT
* *
52899 AATCAGTAAAAGGGAAAAATGGT
1 AATCAGTAAAA-AGTAAAA-GGT
* *
52922 AATCAGTAAAAAATAAAAGAAT
1 AATCAGTAAAAAGTAAAAG-GT
** *
52944 AATCAGTAACGAGTAATTA-GT
1 AATCAGTAAAAAGTAA-AAGGT
* *
52965 AA--AGAAAAAGAGTAAAAAGT
1 AATCAGTAAAA-AGTAAAAGGT
** **
52985 AAAAAAGTAATTAGT-AAAGAGT
1 -AATCAGTAAAAAGTAAAAG-GT
*
53007 AAAAT-GGTAAAAAGT-AAAGAGT
1 --AATCAGTAAAAAGTAAAAG-GT
* **
53029 AACCAGTAAAGAGAAAAAAAAGGT
1 AATCAGT-AA-A-AAGTAAAAGGT
* * *
53053 AATTAGCAAAGAGTAAAAAGGT
1 AATCAGTAAAAAGT-AAAAGGT
* * *
53075 AATCACTAAGAAGTAAGAGGT
1 AATCAGTAAAAAGTAAAAGGT
* *
53096 AATCGGTAAGAAGTAAAAGGT
1 AATCAGTAAAAAGTAAAAGGT
*
53117 AATCAGT-AAGAGTAAATAGGT
1 AATCAGTAAAAAGTAAA-AGGT
* *
53138 AATCAGTAAAGAGTAAAAAGCT
1 AATCAGTAAAAAGT-AAAAGGT
*
53160 AATCAGTAAGAAGTAAAAGGT
1 AATCAGTAAAAAGTAAAAGGT
*
53181 AATCAGTAAAAAAAAAGCGAAAAGGT
1 AATCAGT----AAAAAG-TAAAAGGT
53207 AATCAGTAAAAAGTAAAAGAGT
1 AATCAGTAAAAAGTAAAAG-GT
*
53229 GATCAGTAAA
1 AATCAGTAAA
53239 GAAAAATGGT
Statistics
Matches: 333, Mismatches: 82, Indels: 64
0.70 0.17 0.13
Matches are distributed among these distances:
19 7 0.02
20 23 0.07
21 96 0.29
22 139 0.42
23 37 0.11
24 8 0.02
25 9 0.03
26 14 0.04
ACGTcount: A:0.57, C:0.05, G:0.21, T:0.17
Consensus pattern (21 bp):
AATCAGTAAAAAGTAAAAGGT
Found at i:52985 original size:7 final size:7
Alignment explanation
Indices: 52965--53030 Score: 51
Period size: 7 Copynumber: 9.0 Consensus size: 7
52955 AGTAATTAGT
*
52965 AAAGAAA
1 AAAGTAA
52972 AAGAGTAA
1 AA-AGTAA
52980 AAAGTAAA
1 AAAGT-AA
52988 AAAGTAA
1 AAAGTAA
**
52995 TTAGTAA
1 AAAGTAA
*
53002 AGAGTAA
1 AAAGTAA
*
53009 AATGGTAA
1 AA-AGTAA
53017 AAAGTAA
1 AAAGTAA
*
53024 AGAGTAA
1 AAAGTAA
53031 CCAGTAAAGA
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
7 28 0.60
8 19 0.40
ACGTcount: A:0.64, C:0.00, G:0.20, T:0.17
Consensus pattern (7 bp):
AAAGTAA
Found at i:53006 original size:29 final size:29
Alignment explanation
Indices: 52971--53072 Score: 98
Period size: 29 Copynumber: 3.4 Consensus size: 29
52961 TAGTAAAGAA
52971 AAAGAGTAAAAAGTAAAAAAGTAATTAGT
1 AAAGAGTAAAAAGTAAAAAAGTAATTAGT
* **
53000 AAAGAGTAAAATGGT-AAAAAGTAAAGAGT
1 AAAGAGTAAAA-AGTAAAAAAGTAATTAGT
** * * *
53029 AACCAGTAAAGAGAAAAAAAAGGTAATTAGC
1 AAAGAGTAAAAAG-TAAAAAA-GTAATTAGT
53060 AAAGAGTAAAAAG
1 AAAGAGTAAAAAG
53073 GTAATCACTA
Statistics
Matches: 55, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
28 1 0.02
29 31 0.56
30 7 0.13
31 16 0.29
ACGTcount: A:0.61, C:0.03, G:0.21, T:0.16
Consensus pattern (29 bp):
AAAGAGTAAAAAGTAAAAAAGTAATTAGT
Found at i:53085 original size:21 final size:22
Alignment explanation
Indices: 53045--53189 Score: 167
Period size: 21 Copynumber: 6.8 Consensus size: 22
53035 TAAAGAGAAA
* *
53045 AAAAAGGTAATTAGCAA-AGAGT
1 AAAAAGGTAATCAGTAAGA-AGT
*
53067 AAAAAGGTAATCACTAAGAAGT
1 AAAAAGGTAATCAGTAAGAAGT
* *
53089 -AAGAGGTAATCGGTAAGAAGT
1 AAAAAGGTAATCAGTAAGAAGT
53110 -AAAAGGTAATCAGTAAG-AGT
1 AAAAAGGTAATCAGTAAGAAGT
*
53130 AAATAGGTAATCAGTAA-AGAGT
1 AAAAAGGTAATCAGTAAGA-AGT
*
53152 AAAAAGCTAATCAGTAAGAAGT
1 AAAAAGGTAATCAGTAAGAAGT
53174 -AAAAGGTAATCAGTAA
1 AAAAAGGTAATCAGTAA
53190 AAAAAAAGCG
Statistics
Matches: 106, Mismatches: 12, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.03
21 63 0.59
22 38 0.36
23 2 0.02
ACGTcount: A:0.52, C:0.06, G:0.23, T:0.19
Consensus pattern (22 bp):
AAAAAGGTAATCAGTAAGAAGT
Found at i:53217 original size:21 final size:20
Alignment explanation
Indices: 53200--53265 Score: 53
Period size: 20 Copynumber: 3.1 Consensus size: 20
53190 AAAAAAAGCG
53200 AAAAGGTAATCAGTAAAAAGT
1 AAAAGGTAATCAGT-AAAAGT
* *
53221 AAAAGAGTGATCAGT-AAAGA
1 AAAAG-GTAATCAGTAAAAGT
**
53241 AAAATGGTAAAGAGTAAAGAGT
1 AAAA-GGTAATCAGTAAA-AGT
53263 AAA
1 AAA
53266 GAAAAGAGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
20 14 0.40
21 8 0.23
22 13 0.37
ACGTcount: A:0.58, C:0.03, G:0.23, T:0.17
Consensus pattern (20 bp):
AAAAGGTAATCAGTAAAAGT
Found at i:53243 original size:26 final size:26
Alignment explanation
Indices: 53214--53384 Score: 99
Period size: 26 Copynumber: 7.0 Consensus size: 26
53204 GGTAATCAGT
*
53214 AAAAAGTAAAAGAGTGATCAGTAAAG
1 AAAAAGTAAAAGAGTAATCAGTAAAG
53240 AAAAATGGT-AAAGAGTAA--AG---AG
1 AAAAA--GTAAAAGAGTAATCAGTAAAG
*
53262 -TAAAG-AAAAGAGTAATCAGTAAAG
1 AAAAAGTAAAAGAGTAATCAGTAAAG
* **
53286 AAAATGGT-AAAGAGTAAAAAGTAAAG
1 AAAA-AGTAAAAGAGTAATCAGTAAAG
*
53312 AGTAAAG-AAAAGAGTAATCAGTAAAG
1 A-AAAAGTAAAAGAGTAATCAGTAAAG
*
53338 --AAGGT-AAAGAGTAGA--A-T-AAG
1 AAAAAGTAAAAGAGTA-ATCAGTAAAG
53358 TAAAAAGTAAAA-AGTAATCAGTAAAG
1 -AAAAAGTAAAAGAGTAATCAGTAAAG
53384 A
1 A
53385 GTAAAATAGT
Statistics
Matches: 110, Mismatches: 12, Indels: 47
0.65 0.07 0.28
Matches are distributed among these distances:
19 10 0.09
20 3 0.03
21 6 0.05
22 4 0.04
23 19 0.17
24 7 0.06
25 6 0.05
26 43 0.39
27 10 0.09
28 2 0.02
ACGTcount: A:0.59, C:0.02, G:0.23, T:0.16
Consensus pattern (26 bp):
AAAAAGTAAAAGAGTAATCAGTAAAG
Found at i:53244 original size:27 final size:27
Alignment explanation
Indices: 53214--53276 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
53204 GGTAATCAGT
* *
53214 AAAAAGTAAAAGAGTGATCAGTAAAGA
1 AAAAAGTAAAAGAGTAAACAGTAAAGA
* *
53241 AAAATGGT-AAAGAGTAAAGAGTAAAGA
1 AAAA-AGTAAAAGAGTAAACAGTAAAGA
*
53268 AAAGAGTAA
1 AAAAAGTAA
53277 TCAGTAAAGA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
26 2 0.07
27 24 0.86
28 2 0.07
ACGTcount: A:0.60, C:0.02, G:0.24, T:0.14
Consensus pattern (27 bp):
AAAAAGTAAAAGAGTAAACAGTAAAGA
Found at i:53259 original size:7 final size:7
Alignment explanation
Indices: 53247--53422 Score: 114
Period size: 7 Copynumber: 25.3 Consensus size: 7
53237 AAGAAAAATG
53247 GTAAAGA
1 GTAAAGA
53254 GTAAAGA
1 GTAAAGA
53261 GTAAAGA
1 GTAAAGA
53268 --AAAGA
1 GTAAAGA
**
53273 GTAATCA
1 GTAAAGA
53280 GTAAAGA
1 GTAAAGA
53287 --AAATG-
1 GTAAA-GA
53292 GTAAAGA
1 GTAAAGA
*
53299 GTAAAAA
1 GTAAAGA
53306 GTAAAGA
1 GTAAAGA
53313 GTAAAGA
1 GTAAAGA
53320 --AAAGA
1 GTAAAGA
**
53325 GTAATCA
1 GTAAAGA
53332 GTAAAGAA
1 GTAAAG-A
53340 GGTAAAGA
1 -GTAAAGA
*
53348 GTAGAATAA
1 GTA-AA-GA
*
53357 GTAAAAA
1 GTAAAGA
*
53364 GTAAAAA
1 GTAAAGA
**
53371 GTAATCA
1 GTAAAGA
53378 GTAAAGA
1 GTAAAGA
*
53385 GTAAAATA
1 GT-AAAGA
53393 GTAAAGA
1 GTAAAGA
**
53400 GTCGAGA
1 GTAAAGA
**
53407 GTAATCA
1 GTAAAGA
53414 GTAAAGA
1 GTAAAGA
53421 GT
1 GT
53423 CAAATGACAA
Statistics
Matches: 131, Mismatches: 25, Indels: 26
0.72 0.14 0.14
Matches are distributed among these distances:
5 13 0.10
6 2 0.02
7 94 0.72
8 12 0.09
9 10 0.08
ACGTcount: A:0.56, C:0.03, G:0.24, T:0.17
Consensus pattern (7 bp):
GTAAAGA
Found at i:53273 original size:19 final size:19
Alignment explanation
Indices: 53249--53350 Score: 96
Period size: 19 Copynumber: 5.8 Consensus size: 19
53239 GAAAAATGGT
53249 AAAGAGTAAAGAGTAAAGA
1 AAAGAGTAAAGAGTAAAGA
**
53268 AAAGAGTAATCAGTAAAGA
1 AAAGAGTAAAGAGTAAAGA
53287 AAATG-GTAAAGAGT----A
1 AAA-GAGTAAAGAGTAAAGA
53302 AAA-AGTAAAGAGTAAAGA
1 AAAGAGTAAAGAGTAAAGA
**
53320 AAAGAGTAATCAGTAAAG-
1 AAAGAGTAAAGAGTAAAGA
53338 -AAG-GTAAAGAGTA
1 AAAGAGTAAAGAGTA
53351 GAATAAGTAA
Statistics
Matches: 68, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
14 9 0.13
15 4 0.06
16 8 0.12
17 3 0.04
18 4 0.06
19 39 0.57
20 1 0.01
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.15
Consensus pattern (19 bp):
AAAGAGTAAAGAGTAAAGA
Found at i:53303 original size:52 final size:49
Alignment explanation
Indices: 53216--53368 Score: 188
Period size: 52 Copynumber: 3.1 Consensus size: 49
53206 TAATCAGTAA
* *
53216 AAAGTAAAAGAGTGATCAGTAAAGAA---AAATG-GTAAAGAGTAAAGAGT
1 AAAG-AAAAGAGTAATCAGTAAAGAAGGTAAA-GAGTAAAAAGTAAAGAGT
53263 AAAGAAAAGAGTAATCAGTAAAGAAAATGGTAAAGAGTAAAAAGTAAAGAGT
1 AAAGAAAAGAGTAATCAGTAAAG--AA-GGTAAAGAGTAAAAAGTAAAGAGT
*
53315 AAAGAAAAGAGTAATCAGTAAAGAAGGTAAAGAGTAGAATAAGTAAAAAGT
1 AAAGAAAAGAGTAATCAGTAAAGAAGGTAAAGAGTA-AA-AAGTAAAGAGT
53366 AAA
1 AAA
53369 AAGTAATCAG
Statistics
Matches: 94, Mismatches: 3, Indels: 14
0.85 0.03 0.13
Matches are distributed among these distances:
46 18 0.19
47 4 0.04
48 2 0.02
49 11 0.12
50 4 0.04
51 14 0.15
52 41 0.44
ACGTcount: A:0.59, C:0.02, G:0.24, T:0.16
Consensus pattern (49 bp):
AAAGAAAAGAGTAATCAGTAAAGAAGGTAAAGAGTAAAAAGTAAAGAGT
Found at i:53410 original size:36 final size:37
Alignment explanation
Indices: 53341--53427 Score: 113
Period size: 36 Copynumber: 2.4 Consensus size: 37
53331 AGTAAAGAAG
*
53341 GTAAAGAGTAGAATAAGTAAAAAGTAAAAAGTAATCA
1 GTAAAGAGTAAAATAAGTAAAAAGTAAAAAGTAATCA
* ** *
53378 GTAAAGAGTAAAAT-AGTAAAGAGTCGAGAGTAATCA
1 GTAAAGAGTAAAATAAGTAAAAAGTAAAAAGTAATCA
*
53414 GTAAAGAGTCAAAT
1 GTAAAGAGTAAAAT
53428 GACAATTGGT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 31 0.70
37 13 0.30
ACGTcount: A:0.54, C:0.05, G:0.22, T:0.20
Consensus pattern (37 bp):
GTAAAGAGTAAAATAAGTAAAAAGTAAAAAGTAATCA
Found at i:53465 original size:25 final size:26
Alignment explanation
Indices: 53436--53491 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
53426 ATGACAATTG
53436 GTAATTAAATTCAA-AGAGTAAAATA
1 GTAATTAAATTCAAGAGAGTAAAATA
*
53461 GTAATTAAATTCAAGAGAGTGAAATA
1 GTAATTAAATTCAAGAGAGTAAAATA
53487 GTAAT
1 GTAAT
53492 CAGTAAAGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 14 0.48
26 15 0.52
ACGTcount: A:0.52, C:0.04, G:0.16, T:0.29
Consensus pattern (26 bp):
GTAATTAAATTCAAGAGAGTAAAATA
Found at i:53517 original size:21 final size:21
Alignment explanation
Indices: 53493--53532 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
53483 AATAGTAATC
*
53493 AGTAAAGAGAAAAGAGTAAAG
1 AGTAAACAGAAAAGAGTAAAG
* *
53514 AGTAATCAGGAAAGAGTAA
1 AGTAAACAGAAAAGAGTAA
53533 GATGACAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.28, T:0.12
Consensus pattern (21 bp):
AGTAAACAGAAAAGAGTAAAG
Found at i:53527 original size:14 final size:14
Alignment explanation
Indices: 53481--53532 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
53471 TCAAGAGAGT
*
53481 GAAATAGTAATCAG
1 GAAAGAGTAATCAG
* * **
53495 TAAAGAGAAAAGAG
1 GAAAGAGTAATCAG
*
53509 TAAAGAGTAATCAG
1 GAAAGAGTAATCAG
53523 GAAAGAGTAA
1 GAAAGAGTAA
53533 GATGACAAAA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.56, C:0.04, G:0.25, T:0.15
Consensus pattern (14 bp):
GAAAGAGTAATCAG
Found at i:53579 original size:36 final size:37
Alignment explanation
Indices: 53502--53594 Score: 109
Period size: 36 Copynumber: 2.5 Consensus size: 37
53492 CAGTAAAGAG
*
53502 AAAAGAGT-AAAGAGTAATCAGGAAAGAGTAAGATGAC
1 AAAA-AGTAAAAGAGTAATCAGGAAAGAGTAAAATGAC
* * * **
53539 AAAAAG-CAAGGAGTAATCAGTAAAGAGTAAAATGGT
1 AAAAAGTAAAAGAGTAATCAGGAAAGAGTAAAATGAC
53575 AAAAAGTAAAAGAGTAATCA
1 AAAAAGTAAAAGAGTAATCA
53595 ATAGAAAGTA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
36 32 0.68
37 15 0.32
ACGTcount: A:0.56, C:0.05, G:0.24, T:0.15
Consensus pattern (37 bp):
AAAAAGTAAAAGAGTAATCAGGAAAGAGTAAAATGAC
Found at i:53689 original size:21 final size:21
Alignment explanation
Indices: 53619--53689 Score: 52
Period size: 21 Copynumber: 3.1 Consensus size: 21
53609 GGTGAAGAGT
* * **
53619 AAATTGTAATCAGTAAAGTGA
1 AAATAGTATTCAGTAAAGAAA
53640 AAATAGTATTCAGTTAAAAAGAGTAA
1 AAATAGTATTCAG-T--AAAGA--AA
*
53666 AAATGGTATTCAGTAAAGAAA
1 AAATAGTATTCAGTAAAGAAA
53687 AAA
1 AAA
53690 AAAGTAAAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
21 16 0.40
22 1 0.03
23 5 0.12
24 4 0.10
25 1 0.03
26 13 0.32
ACGTcount: A:0.54, C:0.04, G:0.17, T:0.25
Consensus pattern (21 bp):
AAATAGTATTCAGTAAAGAAA
Found at i:53690 original size:31 final size:32
Alignment explanation
Indices: 53655--53714 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
53645 GTATTCAGTT
*
53655 AAAAAGAGTAAA-AATGGTATTCAGTAAAGAA
1 AAAAAAAGTAAAGAATGGTATTCAGTAAAGAA
53686 AAAAAAAGTAAAGAATGGTATTCAGTAAA
1 AAAAAAAGTAAAGAATGGTATTCAGTAAA
53715 AAAGTAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 11 0.41
32 16 0.59
ACGTcount: A:0.58, C:0.03, G:0.18, T:0.20
Consensus pattern (32 bp):
AAAAAAAGTAAAGAATGGTATTCAGTAAAGAA
Found at i:53723 original size:24 final size:27
Alignment explanation
Indices: 53687--53751 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 27
53677 AGTAAAGAAA
* *
53687 AAAAAAGTAAAG-AATGG-TATTCAGT
1 AAAAAAGTAAAGAAAAGGATAATCAGT
53712 AAAAAAGT-AAGAAAAGGATAATCAGT
1 AAAAAAGTAAAGAAAAGGATAATCAGT
*
53738 AAAAAA-AAAAGAAA
1 AAAAAAGTAAAGAAA
53752 GAAAAAAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 3 0.09
25 12 0.35
26 19 0.56
ACGTcount: A:0.65, C:0.03, G:0.17, T:0.15
Consensus pattern (27 bp):
AAAAAAGTAAAGAAAAGGATAATCAGT
Found at i:53797 original size:28 final size:27
Alignment explanation
Indices: 53765--53868 Score: 72
Period size: 26 Copynumber: 3.8 Consensus size: 27
53755 AAAAGAAGGA
53765 AAAGAAAAGTAAGAAAATGGTAATAAGT
1 AAAGAAAAGT-AGAAAATGGTAATAAGT
* * *
53793 AAAGAAGAGTA-AAAATAGTAATCAGT
1 AAAGAAAAGTAGAAAATGGTAATAAGT
** * *
53819 AAA-AGGAGTAAGAAAA--ATAATTAGT
1 AAAGAAAAGT-AGAAAATGGTAATAAGT
53844 AAGAGAAGAAGGTAGAAAATGGTAA
1 AA-AGAA-AA-GTAGAAAATGGTAA
53869 AAGGGAGTAG
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
25 14 0.24
26 18 0.31
27 6 0.10
28 16 0.27
29 2 0.03
30 3 0.05
ACGTcount: A:0.59, C:0.01, G:0.23, T:0.17
Consensus pattern (27 bp):
AAAGAAAAGTAGAAAATGGTAATAAGT
Found at i:53814 original size:26 final size:26
Alignment explanation
Indices: 53778--53852 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 26
53768 GAAAAGTAAG
*
53778 AAAATGGTAATAAGTAAAGAAGAGTA
1 AAAATAGTAATAAGTAAAGAAGAGTA
* *
53804 AAAATAGTAATCAGTAAA-AGGAGTA
1 AAAATAGTAATAAGTAAAGAAGAGTA
* *
53829 AGAAA-AATAATTAGTAAGAGAAGA
1 A-AAATAGTAATAAGTAA-AGAAGA
53853 AGGTAGAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
25 17 0.43
26 20 0.50
27 3 0.08
ACGTcount: A:0.59, C:0.01, G:0.21, T:0.19
Consensus pattern (26 bp):
AAAATAGTAATAAGTAAAGAAGAGTA
Found at i:53839 original size:25 final size:26
Alignment explanation
Indices: 53785--53852 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 26
53775 AAGAAAATGG
*
53785 TAATAAGTAAAGAAGAGTAAAAATAG
1 TAATAAGTAAAGAAGAGTAAAAATAA
* *
53811 TAATCAGTAAA-AGGAGTAAGAAA-AA
1 TAATAAGTAAAGAAGAGTAA-AAATAA
*
53836 TAATTAGTAAGAGAAGA
1 TAATAAGTAA-AGAAGA
53853 AGGTAGAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
25 17 0.50
26 14 0.41
27 3 0.09
ACGTcount: A:0.59, C:0.01, G:0.21, T:0.19
Consensus pattern (26 bp):
TAATAAGTAAAGAAGAGTAAAAATAA
Found at i:57104 original size:25 final size:26
Alignment explanation
Indices: 57037--57108 Score: 83
Period size: 25 Copynumber: 2.7 Consensus size: 26
57027 AAGAAGACTC
* *
57037 AAAATTTTATAAATTTTTTTAATTCAA
1 AAAATTTTATAAA-CTTTTGAATTCAA
*
57064 AAAAGTTTTTATAAACTTTTGATTTC-A
1 AAAA--TTTTATAAACTTTTGAATTCAA
57091 AAAATTTTATAAACTTTT
1 AAAATTTTATAAACTTTT
57109 ATCTCCTCCT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
25 14 0.35
27 9 0.22
28 8 0.20
29 9 0.22
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.50
Consensus pattern (26 bp):
AAAATTTTATAAACTTTTGAATTCAA
Found at i:58147 original size:43 final size:43
Alignment explanation
Indices: 58100--58223 Score: 169
Period size: 43 Copynumber: 2.9 Consensus size: 43
58090 CCCGAACAAG
* * * *
58100 GGAGAAC-GACAACATTGTAGATTGGTAGAAGTGTCAGAACATA
1 GGAGAACAGA-AACATCGAAGATCGGCAGAAGTGTCAGAACATA
*
58143 GGAGAACAGAAACCTCGAAGATCGGCAGAAGTGTCAGAACATA
1 GGAGAACAGAAACATCGAAGATCGGCAGAAGTGTCAGAACATA
* *
58186 GGAGGACAGAAACATCAAAGATCGGCAGAAGTGTCAGA
1 GGAGAACAGAAACATCGAAGATCGGCAGAAGTGTCAGA
58224 TATGTAGATC
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
43 70 0.97
44 2 0.03
ACGTcount: A:0.41, C:0.15, G:0.29, T:0.15
Consensus pattern (43 bp):
GGAGAACAGAAACATCGAAGATCGGCAGAAGTGTCAGAACATA
Found at i:58434 original size:151 final size:150
Alignment explanation
Indices: 58275--58620 Score: 389
Period size: 151 Copynumber: 2.3 Consensus size: 150
58265 TCGCTGTAAG
58275 ACCCGAACATAGGAGAACGACAACATTGTAAATCGGCAAAAGTGGACGTACGACCCGAACATGGA
1 ACCCGAACATAGGAGAACGACAACATTGTAAATCGGCAAAAGTGGACGTACGACCCGAACATGGA
* * *
58340 AGAACGGATACATCATATATGGGCATAGTGTCAGATATGAAGACCCTTACGA-TGATTACAAATT
66 AGAACGGATACATCATAGATGGGCAGAGTGTCAGATATGAAGACCCTTAC-ATTGATTACAAACT
*
58404 TCAAAGATTTAATG-GGCGTAGA
130 TCAAAGATTTAATGAGAC--AGA
*** * *
58426 ACCCGAACATAGGAGAAC-AGCAACATTGTAAATTAACGAAAA-TGGCCGTAGGACCCGAACATG
1 ACCCGAACATAGGAGAACGA-CAACATTGTAAATCGGC-AAAAGTGGACGTACGACCCGAACATG
* * * * * * * *
58489 GGAGAACGGATACATCGTAGATTGGTAGAGTGTTAGATATGGAGATCCTTACATTGATTACAGAC
64 GAAGAACGGATACATCATAGATGGGCAGAGTGTCAGATATGAAGACCCTTACATTGATTACAAAC
* *
58554 TTGAAAGATTTGATGATGACAGA
129 TTCAAAGATTTAATGA-GACAGA
* *
58577 ATCCGAACAT-GGAAGAACGACAACATTG-AAGATCGGCAGAAGTG
1 ACCCGAACATAGG-AGAACGACAACATTGTAA-ATCGGCAAAAGTG
58621 TCAGATATGG
Statistics
Matches: 162, Mismatches: 24, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
150 9 0.06
151 146 0.90
152 5 0.03
153 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.21
Consensus pattern (150 bp):
ACCCGAACATAGGAGAACGACAACATTGTAAATCGGCAAAAGTGGACGTACGACCCGAACATGGA
AGAACGGATACATCATAGATGGGCAGAGTGTCAGATATGAAGACCCTTACATTGATTACAAACTT
CAAAGATTTAATGAGACAGA
Found at i:60515 original size:99 final size:99
Alignment explanation
Indices: 60344--61146 Score: 1121
Period size: 99 Copynumber: 8.1 Consensus size: 99
60334 ATTTCAAGGA
* * * * *
60344 GACCTTAGCTTTCGATCCGGACACCTCGTGAGAACATCGAGACTAAGTTGGCCGAATGTAAGCCC
1 GACCTTAGATTTCGATCCGGACTCCTCATGAGAACATCGAAACTAAGTTGGCCGAACGTAAGCCC
* ** *
60409 TGCACTCTTTGTGAGAACAAC-AACGTTCATAATT
66 TGGACTCTTTGTGAGAACGGCTAA-GTTCGTAATT
* * * *
60443 GACCTTAGATTTCGATCCGGACACCCCGTGAGAACATCGAAACTAAGTTGGCCGAATGTAAGCCC
1 GACCTTAGATTTCGATCCGGACTCCTCATGAGAACATCGAAACTAAGTTGGCCGAACGTAAGCCC
60508 TGGACTCTTTGTGAGAACGGCTAAGTTCGTAATT
66 TGGACTCTTTGTGAGAACGGCTAAGTTCGTAATT
* * *
60542 GACCTTAGATTCCGATCCAGACTCATCATGAGAACATCGAAACTAAGTTGTGGCCGAACGTAAGC
1 GACCTTAGATTTCGATCCGGACTCCTCATGAGAACATCGAAACTAAG-T-TGGCCGAACGTAAGC
* *
60607 CCTGGACTCTTTGTGAGAAC-GATAACATTCGTAATT
64 CCTGGACTCTTTGTGAGAACGGCTAA-GTTCGTAATT
* * * * *
60643 GACCTTAGATTTCGATCCGGACTCCCCGTGCGAACATCGAAACTAAGTTGGCCAAATGTAAGCCC
1 GACCTTAGATTTCGATCCGGACTCCTCATGAGAACATCGAAACTAAGTTGGCCGAACGTAAGCCC
*
60708 TGGACTCGTTGTGAGAACGGCTAAGTTCGTAATT
66 TGGACTCTTTGTGAGAACGGCTAAGTTCGTAATT
* *
60742 GACCTTAGATTTCGATCCGGACTCATCATGAGAACATCGAAACTAAGTTGTGGTCGAACGTAAGC
1 GACCTTAGATTTCGATCCGGACTCCTCATGAGAACATCGAAACTAAG-T-TGGCCGAACGTAAGC
60807 CCTGGACTCTTTGTGAGAACGGC-AACGTTCGTAATT
64 CCTGGACTCTTTGTGAGAACGGCTAA-GTTCGTAATT
60843 GACCTTAGATTTCGATCCGGACTCC-CATGAGAACATCGAAACTAAGTTGGCCGAACGTAAGCCC
1 GACCTTAGATTTCGATCCGGACTCCTCATGAGAACATCGAAACTAAGTTGGCCGAACGTAAGCCC
*
60907 TGGACTCTTTGTGAGAGCGGCTAAGTTCGTAATT
66 TGGACTCTTTGTGAGAACGGCTAAGTTCGTAATT
* * * * *
60941 GACCTTAGATTTCGATCCAGACTCGTCATGAGAACATTGAAACAAAGTTGTCCGAACGTAAGCCC
1 GACCTTAGATTTCGATCCGGACTCCTCATGAGAACATCGAAACTAAGTTGGCCGAACGTAAGCCC
*
61006 TGGAC-CATTTGTAAGAACGGCTAAGTTCGTAATT
66 TGGACTC-TTTGTGAGAACGGCTAAGTTCGTAATT
* * *
61040 AACCTTAGATTTCGATCCGGACTCGTCATGAGAACATCGAAACTAAGTTGTTGTCGAACGTAAGC
1 GACCTTAGATTTCGATCCGGACTCCTCATGAGAACATCGAAACTAAGTTG--GCCGAACGTAAGC
* * * *
61105 CCTGAACACTTTGTGAGAATGGCTAAGTTCGTATTT
64 CCTGGACTCTTTGTGAGAACGGCTAAGTTCGTAATT
61141 GACCTT
1 GACCTT
61147 TGATCCGGAC
Statistics
Matches: 634, Mismatches: 56, Indels: 26
0.89 0.08 0.04
Matches are distributed among these distances:
98 70 0.11
99 329 0.52
100 36 0.06
101 198 0.31
102 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (99 bp):
GACCTTAGATTTCGATCCGGACTCCTCATGAGAACATCGAAACTAAGTTGGCCGAACGTAAGCCC
TGGACTCTTTGTGAGAACGGCTAAGTTCGTAATT
Found at i:60685 original size:200 final size:200
Alignment explanation
Indices: 60344--61146 Score: 1179
Period size: 200 Copynumber: 4.0 Consensus size: 200
60334 ATTTCAAGGA
* * * * * * *
60344 GACCTTAGCTTTCGATCCGGACACCTCGTGAGAACATCGAGACTAAG-T-TGGCCGAATGTAAGC
1 GACCTTAGATTTCGATCCAGACTCATCATGAGAACATCGAAACTAAGTTGTGGCCGAACGTAAGC
* * * * *
60407 CCTGCACTCTTTGTGAGAACAACAACGTTCATAATTGACCTTAGATTTCGATCCGGACACCCCGT
66 CCTGGACTCTTTGTGAGAACGACAACGTTCGTAATTGACCTTAGATTTCGATCCGGACTCCCCAT
*
60472 GAGAACATCGAAACTAAGTTGGCCGAATGTAAGCCCTGGACTCTTTGTGAGAACGGCTAAGTTCG
131 GAGAACATCGAAACTAAGTTGGCCGAACGTAAGCCCTGGACTCTTTGTGAGAACGGCTAAGTTCG
60537 TAATT
196 TAATT
*
60542 GACCTTAGATTCCGATCCAGACTCATCATGAGAACATCGAAACTAAGTTGTGGCCGAACGTAAGC
1 GACCTTAGATTTCGATCCAGACTCATCATGAGAACATCGAAACTAAGTTGTGGCCGAACGTAAGC
* * *
60607 CCTGGACTCTTTGTGAGAACGATAACATTCGTAATTGACCTTAGATTTCGATCCGGACTCCCCGT
66 CCTGGACTCTTTGTGAGAACGACAACGTTCGTAATTGACCTTAGATTTCGATCCGGACTCCCCAT
* * * *
60672 GCGAACATCGAAACTAAGTTGGCCAAATGTAAGCCCTGGACTCGTTGTGAGAACGGCTAAGTTCG
131 GAGAACATCGAAACTAAGTTGGCCGAACGTAAGCCCTGGACTCTTTGTGAGAACGGCTAAGTTCG
60737 TAATT
196 TAATT
* *
60742 GACCTTAGATTTCGATCCGGACTCATCATGAGAACATCGAAACTAAGTTGTGGTCGAACGTAAGC
1 GACCTTAGATTTCGATCCAGACTCATCATGAGAACATCGAAACTAAGTTGTGGCCGAACGTAAGC
*
60807 CCTGGACTCTTTGTGAGAACGGCAACGTTCGTAATTGACCTTAGATTTCGATCCGGACT-CCCAT
66 CCTGGACTCTTTGTGAGAACGACAACGTTCGTAATTGACCTTAGATTTCGATCCGGACTCCCCAT
*
60871 GAGAACATCGAAACTAAGTTGGCCGAACGTAAGCCCTGGACTCTTTGTGAGAGCGGCTAAGTTCG
131 GAGAACATCGAAACTAAGTTGGCCGAACGTAAGCCCTGGACTCTTTGTGAGAACGGCTAAGTTCG
60936 TAATT
196 TAATT
* * *
60941 GACCTTAGATTTCGATCCAGACTCGTCATGAGAACATTGAAACAAAGTTGT--CCGAACGTAAGC
1 GACCTTAGATTTCGATCCAGACTCATCATGAGAACATCGAAACTAAGTTGTGGCCGAACGTAAGC
* * * **
61004 CCTGGAC-CATTTGTAAGAACGGCTAA-GTTCGTAATTAACCTTAGATTTCGATCCGGACTCGTC
66 CCTGGACTC-TTTGTGAGAACGAC-AACGTTCGTAATTGACCTTAGATTTCGATCCGGACTCCCC
* * * *
61067 ATGAGAACATCGAAACTAAGTTGTTGTCGAACGTAAGCCCTGAACACTTTGTGAGAATGGCTAAG
129 ATGAGAACATCGAAACTAAGTTG--GCCGAACGTAAGCCCTGGACTCTTTGTGAGAACGGCTAAG
*
61132 TTCGTATTT
192 TTCGTAATT
61141 GACCTT
1 GACCTT
61147 TGATCCGGAC
Statistics
Matches: 554, Mismatches: 44, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
196 1 0.00
197 63 0.11
198 66 0.12
199 117 0.21
200 307 0.55
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (200 bp):
GACCTTAGATTTCGATCCAGACTCATCATGAGAACATCGAAACTAAGTTGTGGCCGAACGTAAGC
CCTGGACTCTTTGTGAGAACGACAACGTTCGTAATTGACCTTAGATTTCGATCCGGACTCCCCAT
GAGAACATCGAAACTAAGTTGGCCGAACGTAAGCCCTGGACTCTTTGTGAGAACGGCTAAGTTCG
TAATT
Found at i:61299 original size:34 final size:34
Alignment explanation
Indices: 61204--61350 Score: 226
Period size: 34 Copynumber: 4.4 Consensus size: 34
61194 CTACGTAGGA
61204 TGCCGAATTGTTATTCTCCCAACTTTCGAGATCT
1 TGCCGAATTGTTATTCTCCCAACTTTCGAGATCT
* *
61238 TGCTGAATTG-T-TTCTCCCAACTCTCGAGATCT
1 TGCCGAATTGTTATTCTCCCAACTTTCGAGATCT
*
61270 TGCCGAATTGTTATTCTCCCACCTTTCGAGATCT
1 TGCCGAATTGTTATTCTCCCAACTTTCGAGATCT
* *
61304 TGTCGAATTGTTAGTCTCCCAACTTTCGAGATCT
1 TGCCGAATTGTTATTCTCCCAACTTTCGAGATCT
*
61338 TGTCGAATTGTTA
1 TGCCGAATTGTTA
61351 ATATTTACAA
Statistics
Matches: 103, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
32 29 0.28
33 2 0.02
34 72 0.70
ACGTcount: A:0.20, C:0.25, G:0.16, T:0.39
Consensus pattern (34 bp):
TGCCGAATTGTTATTCTCCCAACTTTCGAGATCT
Found at i:61312 original size:66 final size:67
Alignment explanation
Indices: 61204--61350 Score: 235
Period size: 66 Copynumber: 2.2 Consensus size: 67
61194 CTACGTAGGA
61204 TGCCGAATTGTTATTCTCCCAACTTTCGAGATCTTGCTGAATTGTT-TCTCCCAACTCTCGAGAT
1 TGCCGAATTGTTATTCTCCCAACTTTCGAGATCTTGCTGAATTGTTATCTCCCAACTCTCGAGAT
61268 CT
66 CT
* *
61270 TGCCGAATTGTTATTCTCCCACCTTTCGAGATCTTG-TCGAATTGTTAGTCTCCCAACTTTCGAG
1 TGCCGAATTGTTATTCTCCCAACTTTCGAGATCTTGCT-GAATTGTTA-TCTCCCAACTCTCGAG
61334 ATCT
64 ATCT
*
61338 TGTCGAATTGTTA
1 TGCCGAATTGTTA
61351 ATATTTACAA
Statistics
Matches: 75, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
65 1 0.01
66 43 0.57
68 31 0.41
ACGTcount: A:0.20, C:0.25, G:0.16, T:0.39
Consensus pattern (67 bp):
TGCCGAATTGTTATTCTCCCAACTTTCGAGATCTTGCTGAATTGTTATCTCCCAACTCTCGAGAT
CT
Found at i:65435 original size:22 final size:21
Alignment explanation
Indices: 65396--65436 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
65386 GCTAGCTCGA
65396 CCGGTAATGACCAGCCACAGC
1 CCGGTAATGACCAGCCACAGC
* *
65417 CCGGTTATGTCCATGCCACA
1 CCGGTAATGACCA-GCCACA
65437 CCGGTATGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.24, C:0.37, G:0.22, T:0.17
Consensus pattern (21 bp):
CCGGTAATGACCAGCCACAGC
Found at i:67601 original size:11 final size:11
Alignment explanation
Indices: 67585--67614 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
67575 GAAGCTCGTG
*
67585 TTTGAAGATTA
1 TTTGAAGATAA
67596 TTTGAAGATAA
1 TTTGAAGATAA
67607 TTTGAAGA
1 TTTGAAGA
67615 ATTGAAGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (11 bp):
TTTGAAGATAA
Found at i:68203 original size:32 final size:32
Alignment explanation
Indices: 68166--68277 Score: 156
Period size: 32 Copynumber: 3.5 Consensus size: 32
68156 TTAAATTCTT
* *
68166 TTATTCTGCTTAATTACCCTGAATTATG-CATC
1 TTATTCTACTTAATTACCCTGAATTAAGCCA-C
68198 TTATTCTACTTAATTACCCTGAATTAAGCCAC
1 TTATTCTACTTAATTACCCTGAATTAAGCCAC
*
68230 TTATTCTACTTAATTACCCTGAATTAAGTTCC-T
1 TTATTCTACTTAATTACCCTGAATTAAG--CCAC
68263 TTATTCTACTTAATT
1 TTATTCTACTTAATT
68278 TCCTTCCCTG
Statistics
Matches: 74, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
32 55 0.74
33 17 0.23
34 2 0.03
ACGTcount: A:0.28, C:0.21, G:0.06, T:0.45
Consensus pattern (32 bp):
TTATTCTACTTAATTACCCTGAATTAAGCCAC
Found at i:68474 original size:151 final size:147
Alignment explanation
Indices: 68328--69044 Score: 755
Period size: 151 Copynumber: 4.9 Consensus size: 147
68318 CCTAATTTCC
* * *
68328 TTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCTAGTCTTTTCTTT
1 TTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTT-TTT
* * * * * *
68393 ACTTAATTTCCCTGAAATTAAGCCACTATTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTTA
65 ACCTAATTTCCTTGAAATTAAGCCAGTATTTTCTTTACCTAATTTCCTTGAAATTAAGTCAGTTA
*
68458 GTCTTCTTTTACCTAATTT
130 GTCTTCTTTTACCTAA-GT
** * * *
68477 CCTTCCTTGAAATTAAGCCAGTCTTTTCTTTATATAGTTTCCTTGAAACTAAGTCAGTCTTTTAT
1 --TTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTT-T
* * *
68542 TTACTTAATTTCCTTGAAACTAAGCCAGTCAGTCTTTTTTTACCTAATTTCCTTCCTTGAAATTA
63 TTACCTAATTTCCTTGAAATTAAGCCAGT-A-T-TTTCTTTACCTAA--T--TTCCTTGAAATTA
* *
68607 AGCCAGTCT--T-TTC-TTTAACT-AGT
121 AGTCAGT-TAGTCTTCTTTTACCTAAGT
* * * *
68630 TTCCTTGAAACTAAGGCAGTCTTTTCTTTACTTAATTTCCCTGAAATTAAGCCAGTCTTTTCTTT
1 TTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTT-TTT
* * * *
68695 ACCTAGTTTCCTTGAAACTAAGTCAGTCAGTCTTCTTTTACCTAATTTCCTTGAAATTAAGTCAG
65 ACCTAATTTCCTTGAAATTAAGCCAGT-A-TTTTC-TTTACCTAATTTCCTTGAAATTAAGTCAG
* *
68760 TCAGTCTCCTTTTACCTAA-T
127 TTAGTCTTCTTTTACCTAAGT
* * * * *
68780 TTCCTTGAAATTAAGTCAATCTTCT-TTTACCTAATTTCCTTGAAATTAAGCCAGTCTTCTTTTG
1 TTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTTTTA
68844 CCTAATTTCCTTGAAATTAAGCCAG--TTTTCTTTTACCTAATTTCCTTGAAATTAAGTCA---A
66 CCTAATTTCCTTGAAATTAAGCCAGTATTTTC-TTTACCTAATTTCCTTGAAATTAAGTCAGTTA
*
68904 -TCTTCTTTTGCCT-AGT
130 GTCTTCTTTTACCTAAGT
* * * * * *
68920 TTCCTTGAAATTAAACTAGTCTTCT-TTTGCCTAATTTCCTTGCAATTAAGCCAGTCTTCTTTTA
1 TTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTTTTA
* * *
68984 CCTAATTTCCTTGAAATTAAGTCAGTCTTCT-TTTACCTAATTTCCTTGAAATTAAGTCAGT
66 CCTAATTTCCTTGAAATTAAGCCAGTATTTTCTTTACCTAATTTCCTTGAAATTAAGTCAGT
69045 CTTTCTTTTA
Statistics
Matches: 493, Mismatches: 54, Indels: 47
0.83 0.09 0.08
Matches are distributed among these distances:
139 1 0.00
140 121 0.25
141 1 0.00
142 3 0.01
144 33 0.07
147 19 0.04
148 26 0.05
149 35 0.07
150 30 0.06
151 178 0.36
152 1 0.00
153 2 0.00
154 12 0.02
155 6 0.01
156 4 0.01
157 1 0.00
158 19 0.04
159 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.10, T:0.44
Consensus pattern (147 bp):
TTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTTTTA
CCTAATTTCCTTGAAATTAAGCCAGTATTTTCTTTACCTAATTTCCTTGAAATTAAGTCAGTTAG
TCTTCTTTTACCTAAGT
Found at i:68500 original size:115 final size:109
Alignment explanation
Indices: 68305--69052 Score: 743
Period size: 115 Copynumber: 6.8 Consensus size: 109
68295 GCATGTGCCT
* * *
68305 CAGTC-TTTCTTTACCTAATTTCCTTCCTTGAAATTAAGCCAGTCTTTTC-TTTACCTAGTTTCC
1 CAGTCTTTTCTTTACCTAA--T--TTCCTTGAAATTAAGCCAGTATCTTCTTTTACCTAATTTCC
* * * *
68368 TTGAAACTAAGCTAGTCTTTTCTTTACTTAATTTCCCTGAAATTAAGC
62 TTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTCCTTGAAATTAAGC
* * * *
68416 CACTATTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTTAGTCTTCTTTTACCTAATTTCCTT
1 CAGTCTTTTCTTTACCTAATTTCCTTGAAATTAAGCCAG-TA-TCTTCTTTTACCTAA--T--TT
** * * *
68481 CCTTGAAATTAAGCCAGTCTTTTCTTTATATAGTTTCCTTGAAACTAAGT
60 CCTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTCCTTGAAATTAAGC
* * * *
68531 CAGTCTTTTATTTACTTAATTTCCTTGAAACTAAGCCAGTCAGTCTTTTTTTACCTAATTTCCTT
1 CAGTCTTTTCTTTACCTAATTTCCTTGAAATTAAGCCAGT-A-TCTTCTTTTACCTAA--T--TT
* * * *
68596 CCTTGAAATTAAGCCAGTCTTTTCTTTAACTAGTTTCCTTGAAACTAAGG
60 CCTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTCCTTGAAATTAAGC
* * * * *
68646 CAGTCTTTTCTTTACTTAATTTCCCTGAAATTAAGCCAGTCTTTTC-TTTACCTAGTTTCCTTGA
1 CAGTCTTTTCTTTACCTAATTTCCTTGAAATTAAGCCAGTATCTTCTTTTACCTAATTTCCTTGA
* * * *
68710 AACTAAGTCAGTCAGTCTTCTTTTACCTAATTTCCTTGAAATTAAGT
66 AATTAAGCCAGTC--TTTTC-TTTACCTAATTTCCTTGAAATTAAGC
* * *
68757 CAGTCAGTCTCCTTTTACCTAATTTCCTTGAAATTAAGTCA--ATCTTCTTTTACCTAATTTCCT
1 CAGTC--TTTTC-TTTACCTAATTTCCTTGAAATTAAGCCAGTATCTTCTTTTACCTAATTTCCT
* *
68820 TGAAATTAAGCCAGTCTTCT-TTTGCCTAATTTCCTTGAAATTAAGC
63 TGAAATTAAGCCAGTCTTTTCTTTACCTAATTTCCTTGAAATTAAGC
* * *
68866 CAG--TTTTCTTTTACCTAATTTCCTTGAAATTAAGTCA--ATCTTCTTTTGCCTAGTTTCCTTG
1 CAGTCTTTTC-TTTACCTAATTTCCTTGAAATTAAGCCAGTATCTTCTTTTACCTAATTTCCTTG
* * * * *
68927 AAATTAAACTAGTCTTCT-TTTGCCTAATTTCCTTGCAATTAAGC
65 AAATTAAGCCAGTCTTTTCTTTACCTAATTTCCTTGAAATTAAGC
* *
68971 CAGTCTTCT-TTTACCTAATTTCCTTGAAATTAAGTCAG--TCTTCTTTTACCTAATTTCCTTGA
1 CAGTCTTTTCTTTACCTAATTTCCTTGAAATTAAGCCAGTATCTTCTTTTACCTAATTTCCTTGA
*
69033 AATTAAGTCAGTC-TTTCTTT
66 AATTAAGCCAGTCTTTTCTTT
69053 TATTCTTACT
Statistics
Matches: 551, Mismatches: 66, Indels: 46
0.83 0.10 0.07
Matches are distributed among these distances:
104 2 0.00
105 161 0.29
107 3 0.01
108 37 0.07
109 28 0.05
110 10 0.02
111 40 0.07
112 24 0.04
113 35 0.06
114 26 0.05
115 185 0.34
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.44
Consensus pattern (109 bp):
CAGTCTTTTCTTTACCTAATTTCCTTGAAATTAAGCCAGTATCTTCTTTTACCTAATTTCCTTGA
AATTAAGCCAGTCTTTTCTTTACCTAATTTCCTTGAAATTAAGC
Found at i:68759 original size:35 final size:35
Alignment explanation
Indices: 68328--69054 Score: 684
Period size: 35 Copynumber: 19.8 Consensus size: 35
68318 CCTAATTTCC
* * *
68328 TTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAGT
1 TTCCTTGAAATTAAGTCAGTCTTCT-TTTACCTAAT
* * *
68364 TTCCTTGAAACTAAG-CTAGTCTTTTCTTTACTTAAT
1 TTCCTTGAAATTAAGTC-AGTCTTCT-TTTACCTAAT
* * * * * *
68400 TTCCCTGAAATTAAGCCACTATTTTCTTTACCTAGT
1 TTCCTTGAAATTAAGTCAGTCTTCT-TTTACCTAAT
* *
68436 TTCCTTGAAACTAAGCCAGTTAGTCTTCTTTTACCTAATTT
1 TTCCTTGAAA-TTA---AGTCAGTCTTCTTTTACCTAA--T
* * ** *
68477 CCTTCCTTGAAATTAAGCCAGTCTTTTCTTTATATAGT
1 --TTCCTTGAAATTAAGTCAGTCTTCT-TTTACCTAAT
* * *
68515 TTCCTTGAAACTAAGTCAGTCTTTTATTTACTTAAT
1 TTCCTTGAAATTAAGTCAGTCTTCT-TTTACCTAAT
* *
68551 TTCCTTGAAACTAAGCCAGTCAGTCTTTTTTTACCTAATTT
1 TTCCTTGAAA-TTA---AGTCAGTCTTCTTTTACCTAA--T
* * * *
68592 CCTTCCTTGAAATTAAGCCAGTCTTTTCTTTAACTAGT
1 --TTCCTTGAAATTAAGTCAGTCTTCT-TTTACCTAAT
* * * *
68630 TTCCTTGAAACTAAGGCAGTCTTTTCTTTACTTAAT
1 TTCCTTGAAATTAAGTCAGTCTTCT-TTTACCTAAT
* * * *
68666 TTCCCTGAAATTAAGCCAGTCTTTTCTTTACCTAGT
1 TTCCTTGAAATTAAGTCAGTCTTCT-TTTACCTAAT
*
68702 TTCCTTGAAACTAAGTCAGTCAGTCTTCTTTTACCTAAT
1 TTCCTTGAAA-T---TAAGTCAGTCTTCTTTTACCTAAT
68741 TTCCTTGAAATTAAGTCAGTCAGTCTCCTTTTACCTAAT
1 TTCCTTGAAATTAAGTCAGTC--T-T-CTTTTACCTAAT
*
68780 TTCCTTGAAATTAAGTCAATCTTCTTTTACCTAAT
1 TTCCTTGAAATTAAGTCAGTCTTCTTTTACCTAAT
* *
68815 TTCCTTGAAATTAAGCCAGTCTTCTTTTGCCTAAT
1 TTCCTTGAAATTAAGTCAGTCTTCTTTTACCTAAT
* *
68850 TTCCTTGAAATTAAGCCAGTTTTCTTTTACCTAAT
1 TTCCTTGAAATTAAGTCAGTCTTCTTTTACCTAAT
* * *
68885 TTCCTTGAAATTAAGTCAATCTTCTTTTGCCTAGT
1 TTCCTTGAAATTAAGTCAGTCTTCTTTTACCTAAT
* *
68920 TTCCTTGAAATTAA-ACTAGTCTTCTTTTGCCTAAT
1 TTCCTTGAAATTAAGTC-AGTCTTCTTTTACCTAAT
* *
68955 TTCCTTGCAATTAAGCCAGTCTTCTTTTACCTAAT
1 TTCCTTGAAATTAAGTCAGTCTTCTTTTACCTAAT
68990 TTCCTTGAAATTAAGTCAGTCTTCTTTTACCTAAT
1 TTCCTTGAAATTAAGTCAGTCTTCTTTTACCTAAT
69025 TTCCTTGAAATTAAGTCAGTCTTTCTTTTA
1 TTCCTTGAAATTAAGTCAGTC-TTCTTTTA
69055 TTCTTACTTA
Statistics
Matches: 588, Mismatches: 72, Indels: 62
0.81 0.10 0.09
Matches are distributed among these distances:
34 1 0.00
35 231 0.39
36 189 0.32
37 7 0.01
38 4 0.01
39 87 0.15
40 43 0.07
41 2 0.00
42 4 0.01
43 20 0.03
ACGTcount: A:0.25, C:0.21, G:0.10, T:0.44
Consensus pattern (35 bp):
TTCCTTGAAATTAAGTCAGTCTTCTTTTACCTAAT
Found at i:69104 original size:40 final size:40
Alignment explanation
Indices: 69058--69161 Score: 129
Period size: 40 Copynumber: 2.6 Consensus size: 40
69048 TCTTTTATTC
* * * * *
69058 TTACTTAATTGCCATGACTTAAGTCCTTTGACTTCTG-TGT
1 TTACTTAATTACCATGAATTAAGTACTTTAACTGCTGCT-T
69098 TTACTTAATTACCATGAATTAAGTACTTTAACTGCTGCTT
1 TTACTTAATTACCATGAATTAAGTACTTTAACTGCTGCTT
* *
69138 TTACTTAATTTCTATGAATTAAGT
1 TTACTTAATTACCATGAATTAAGT
69162 GCTCTAATTG
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 55 0.98
41 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (40 bp):
TTACTTAATTACCATGAATTAAGTACTTTAACTGCTGCTT
Done.