Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009395.1 Corchorus capsularis cultivar CVL-1 contig09416, 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: 68199
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:62 original size:22 final size:22
Alignment explanation
Indices: 21--210 Score: 133
Period size: 22 Copynumber: 9.1 Consensus size: 22
11 AAAGTAATGA
*
21 TAATCAGTAAA-AGTAAAATAG
1 TAATCAGTAAAGAATAAAATAG
42 TAATCAGTAAAGAATAAAATAG
1 TAATCAGTAAAGAATAAAATAG
*
64 TAATCAGTAAA-AAGTAAGAA-GG
1 TAATCAGTAAAGAA-TAA-AATAG
*
86 TAATCAGTAAAGAGTAAAATAG
1 TAATCAGTAAAGAATAAAATAG
** *
108 TAAAAAGTAATG-AT--AATCAG
1 TAATCAGTAAAGAATAAAAT-AG
*
128 T-A--A--A-AGTA-A-AATAG
1 TAATCAGTAAAGAATAAAATAG
*
142 TAATCAGTAAAGAGTAAAATAG
1 TAATCAGTAAAGAATAAAATAG
*
164 TAATCAGTAAA-AAGTAAGAA-GG
1 TAATCAGTAAAGAA-TAA-AATAG
*
186 TAATCAGTAAAGAGTAAAATAG
1 TAATCAGTAAAGAATAAAATAG
208 TAA
1 TAA
211 AAAGTGATGA
Statistics
Matches: 134, Mismatches: 15, Indels: 39
0.71 0.08 0.21
Matches are distributed among these distances:
14 4 0.03
15 6 0.04
17 2 0.01
19 5 0.04
20 5 0.04
21 20 0.15
22 86 0.64
23 6 0.04
ACGTcount: A:0.56, C:0.04, G:0.17, T:0.22
Consensus pattern (22 bp):
TAATCAGTAAAGAATAAAATAG
Found at i:111 original size:8 final size:7
Alignment explanation
Indices: 29--215 Score: 83
Period size: 7 Copynumber: 25.9 Consensus size: 7
19 GATAATCAGT
29 AAAAGTA
1 AAAAGTA
36 AAATAGTA
1 AAA-AGTA
**
44 ATCAGTA
1 AAAAGTA
51 AAGAA-TA
1 AA-AAGTA
58 AAATAGTA
1 AAA-AGTA
**
66 ATCAGTA
1 AAAAGTA
73 AAAAGTA
1 AAAAGTA
*
80 AGAAGGTA
1 A-AAAGTA
**
88 ATCAGTA
1 AAAAGTA
*
95 AAGAGTA
1 AAAAGTA
102 AAATAGTA
1 AAA-AGTA
110 AAAAGTA
1 AAAAGTA
**
117 ATGA-TA
1 AAAAGTA
**
123 ATCAGT-
1 AAAAGTA
129 AAAAGTA
1 AAAAGTA
136 AAATAGTA
1 AAA-AGTA
**
144 ATCAGTA
1 AAAAGTA
*
151 AAGAGTA
1 AAAAGTA
158 AAATAGTA
1 AAA-AGTA
**
166 ATCAGTA
1 AAAAGTA
173 AAAAGTA
1 AAAAGTA
*
180 AGAAGGTA
1 A-AAAGTA
**
188 ATCAGTA
1 AAAAGTA
*
195 AAGAGTA
1 AAAAGTA
202 AAATAGTA
1 AAA-AGTA
210 AAAAGT
1 AAAAGT
216 GATGATAATC
Statistics
Matches: 132, Mismatches: 36, Indels: 24
0.69 0.19 0.12
Matches are distributed among these distances:
6 10 0.08
7 77 0.58
8 45 0.34
ACGTcount: A:0.57, C:0.04, G:0.18, T:0.21
Consensus pattern (7 bp):
AAAAGTA
Found at i:174 original size:100 final size:100
Alignment explanation
Indices: 1--358 Score: 582
Period size: 100 Copynumber: 3.6 Consensus size: 100
**
1 AAAATAGTAAAAAGTAATGATAATCAGTAAAAGTAAAATAGTAATCAGTAAAGAATAAAATAGTA
1 AAAATAGTAAAAAGTAATGATAATCAGTAAAAGTAAAATAGTAATCAGTAAAGAGCAAAATAGTA
66 ATCAGTAAAAAGTAAGAAGGTAATCAGTAAAGAGT
66 ATCAGTAAAAAGTAAGAAGGTAATCAGTAAAGAGT
*
101 AAAATAGTAAAAAGTAATGATAATCAGTAAAAGTAAAATAGTAATCAGTAAAGAGTAAAATAGTA
1 AAAATAGTAAAAAGTAATGATAATCAGTAAAAGTAAAATAGTAATCAGTAAAGAGCAAAATAGTA
166 ATCAGTAAAAAGTAAGAAGGTAATCAGTAAAGAGT
66 ATCAGTAAAAAGTAAGAAGGTAATCAGTAAAGAGT
* *
201 AAAATAGTAAAAAGTGATGATAATCAGTAAAAAGTAAAATGGTAATCAGT-AAGAGCAAAATAGT
1 AAAATAGTAAAAAGTAATGATAATCAGT-AAAAGTAAAATAGTAATCAGTAAAGAGCAAAATAGT
* * *
265 AAACAGTAAAAAGTAAGAAGGTAATCAATAAAGAAT
65 AATCAGTAAAAAGTAAGAAGGTAATCAGTAAAGAGT
*
301 AAAATAGT-AAAA--AA-GGTAATCAGTAAAAGGTAAAATAGTAATCAGTAAAGAGCAAAAT
1 AAAATAGTAAAAAGTAATGATAATCAGTAAAA-GTAAAATAGTAATCAGTAAAGAGCAAAAT
359 GGTTATTAGT
Statistics
Matches: 245, Mismatches: 10, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
95 4 0.02
96 25 0.10
97 12 0.05
99 4 0.02
100 180 0.73
101 20 0.08
ACGTcount: A:0.57, C:0.04, G:0.18, T:0.21
Consensus pattern (100 bp):
AAAATAGTAAAAAGTAATGATAATCAGTAAAAGTAAAATAGTAATCAGTAAAGAGCAAAATAGTA
ATCAGTAAAAAGTAAGAAGGTAATCAGTAAAGAGT
Found at i:249 original size:22 final size:22
Alignment explanation
Indices: 221--310 Score: 87
Period size: 22 Copynumber: 4.1 Consensus size: 22
211 AAAGTGATGA
*
221 TAATCAGTAAAAAGTAAAATGG
1 TAATCAGTAAAAAGTAAAATAG
* *
243 TAATCAGT-AAGAGCAAAATAG
1 TAATCAGTAAAAAGTAAAATAG
* *
264 TAAACAGTAAAAAGTAAGAA-GG
1 TAATCAGTAAAAAGTAA-AATAG
*
286 TAATCAATAAAGAA-TAAAATAG
1 TAATCAGTAAA-AAGTAAAATAG
308 TAA
1 TAA
311 AAAAGGTAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
21 19 0.35
22 31 0.57
23 4 0.07
ACGTcount: A:0.58, C:0.06, G:0.17, T:0.20
Consensus pattern (22 bp):
TAATCAGTAAAAAGTAAAATAG
Found at i:266 original size:21 final size:21
Alignment explanation
Indices: 221--275 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
211 AAAGTGATGA
* *
221 TAATCAGTAAAAAGTAAAATGG
1 TAATCAGT-AAAAGCAAAATAG
*
243 TAATCAGTAAGAGCAAAATAG
1 TAATCAGTAAAAGCAAAATAG
*
264 TAAACAGTAAAA
1 TAATCAGTAAAA
276 AGTAAGAAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 20 0.71
22 8 0.29
ACGTcount: A:0.56, C:0.07, G:0.16, T:0.20
Consensus pattern (21 bp):
TAATCAGTAAAAGCAAAATAG
Found at i:273 original size:28 final size:27
Alignment explanation
Indices: 169--282 Score: 81
Period size: 28 Copynumber: 4.0 Consensus size: 27
159 AATAGTAATC
169 AGTAAAA-AGTAAGAAGGTAATCAGTAAAG
1 AGTAAAATAGTAA-AA-GTAATCAGT-AAG
* * *
198 AGTAAAATAGTAAAAAGTGATGA-TAATC
1 AGTAAAATAGT-AAAAGTAATCAGTAA-G
226 AGTAAAA-AGTAAAATGGTAATCAGTAAG
1 AGTAAAATAGTAAAA--GTAATCAGTAAG
* **
254 AGCAAAATAGTAAACAGTAAAAAGTAAG
1 AGTAAAATAGTAAA-AGTAATCAGTAAG
282 A
1 A
283 AGGTAATCAA
Statistics
Matches: 68, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
26 4 0.06
27 5 0.07
28 30 0.44
29 21 0.31
30 6 0.09
31 2 0.03
ACGTcount: A:0.56, C:0.04, G:0.20, T:0.19
Consensus pattern (27 bp):
AGTAAAATAGTAAAAGTAATCAGTAAG
Found at i:320 original size:31 final size:31
Alignment explanation
Indices: 282--341 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
272 AAAAAGTAAG
282 AAGGTAATCAAT-AAAGAATAAAATAGTAAAA
1 AAGGTAATCAATAAAAG-ATAAAATAGTAAAA
* *
313 AAGGTAATCAGTAAAAGGTAAAATAGTAA
1 AAGGTAATCAATAAAAGATAAAATAGTAA
342 TCAGTAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.60, C:0.03, G:0.17, T:0.20
Consensus pattern (31 bp):
AAGGTAATCAATAAAAGATAAAATAGTAAAA
Found at i:341 original size:22 final size:22
Alignment explanation
Indices: 307--392 Score: 77
Period size: 22 Copynumber: 3.9 Consensus size: 22
297 GAATAAAATA
*
307 GTAAAAAAGGTAATCAGTAAAAG
1 GTAAAATA-GTAATCAGTAAAAG
330 GTAAAATAGTAATCAGT-AAAG
1 GTAAAATAGTAATCAGTAAAAG
* * * * *
351 AGCAAAATGGTTATTAGTAAGA-
1 -GTAAAATAGTAATCAGTAAAAG
*
373 GTAAAATAGTAATCTGTAAA
1 GTAAAATAGTAATCAGTAAA
393 GAGTGAAAGG
Statistics
Matches: 49, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
21 18 0.37
22 22 0.45
23 9 0.18
ACGTcount: A:0.51, C:0.05, G:0.20, T:0.24
Consensus pattern (22 bp):
GTAAAATAGTAATCAGTAAAAG
Found at i:3486 original size:172 final size:172
Alignment explanation
Indices: 3200--3543 Score: 688
Period size: 172 Copynumber: 2.0 Consensus size: 172
3190 GTTTCTTGGT
3200 TTTAAGTATATTAATGAATTGTATGCTAGTGATGTTTATTTTGGTGAAATATTTAAAGCATGTGA
1 TTTAAGTATATTAATGAATTGTATGCTAGTGATGTTTATTTTGGTGAAATATTTAAAGCATGTGA
3265 AAATTCTGGATTTGGAAAGTATTATAAGCATGATGGATTTTTGTTTAAGGAATCTAGATTGTGTG
66 AAATTCTGGATTTGGAAAGTATTATAAGCATGATGGATTTTTGTTTAAGGAATCTAGATTGTGTG
3330 TGCCTTCTTTTTCTTTGCGCATCTTGCTCATGAGGGAATCGC
131 TGCCTTCTTTTTCTTTGCGCATCTTGCTCATGAGGGAATCGC
3372 TTTAAGTATATTAATGAATTGTATGCTAGTGATGTTTATTTTGGTGAAATATTTAAAGCATGTGA
1 TTTAAGTATATTAATGAATTGTATGCTAGTGATGTTTATTTTGGTGAAATATTTAAAGCATGTGA
3437 AAATTCTGGATTTGGAAAGTATTATAAGCATGATGGATTTTTGTTTAAGGAATCTAGATTGTGTG
66 AAATTCTGGATTTGGAAAGTATTATAAGCATGATGGATTTTTGTTTAAGGAATCTAGATTGTGTG
3502 TGCCTTCTTTTTCTTTGCGCATCTTGCTCATGAGGGAATCGC
131 TGCCTTCTTTTTCTTTGCGCATCTTGCTCATGAGGGAATCGC
3544 ATGAAGGGGG
Statistics
Matches: 172, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
172 172 1.00
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42
Consensus pattern (172 bp):
TTTAAGTATATTAATGAATTGTATGCTAGTGATGTTTATTTTGGTGAAATATTTAAAGCATGTGA
AAATTCTGGATTTGGAAAGTATTATAAGCATGATGGATTTTTGTTTAAGGAATCTAGATTGTGTG
TGCCTTCTTTTTCTTTGCGCATCTTGCTCATGAGGGAATCGC
Found at i:5058 original size:22 final size:22
Alignment explanation
Indices: 5001--5086 Score: 91
Period size: 22 Copynumber: 3.9 Consensus size: 22
4991 AGTAGGACAT
* *
5001 GTTCTGGGTAGAAGTTGTTCAA
1 GTTCTGGGCAGAAGTTGTCCAA
** *
5023 GTTGAGGGCGGAAGTTGTCCAA
1 GTTCTGGGCAGAAGTTGTCCAA
* *
5045 GTTCTGGACAGAAGTTGTACAA
1 GTTCTGGGCAGAAGTTGTCCAA
* *
5067 GTTCTAGGCAGAACTTGTCC
1 GTTCTGGGCAGAAGTTGTCC
5087 TACATTTTTT
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.24, C:0.15, G:0.31, T:0.29
Consensus pattern (22 bp):
GTTCTGGGCAGAAGTTGTCCAA
Found at i:5085 original size:44 final size:44
Alignment explanation
Indices: 5001--5086 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 44
4991 AGTAGGACAT
** * * *
5001 GTTCTGGGTAGAAGTTGTTCAAGTTGAGGGCGGAAGTTGTCCAA
1 GTTCTGGACAGAAGTTGTACAAGTTGAGGGCAGAACTTGTCCAA
*
5045 GTTCTGGACAGAAGTTGTACAAGTTCTA-GGCAGAACTTGTCC
1 GTTCTGGACAGAAGTTGTACAAGTT-GAGGGCAGAACTTGTCC
5087 TACATTTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 34 0.97
45 1 0.03
ACGTcount: A:0.24, C:0.15, G:0.31, T:0.29
Consensus pattern (44 bp):
GTTCTGGACAGAAGTTGTACAAGTTGAGGGCAGAACTTGTCCAA
Found at i:9906 original size:29 final size:31
Alignment explanation
Indices: 9852--9929 Score: 83
Period size: 29 Copynumber: 2.6 Consensus size: 31
9842 CAAACATTTT
* *
9852 ATCAATCAGTTAGCAA-ATAATTGCAATTC-A
1 ATCAATCA-ATAGCAAGATAATGGCAATTCAA
9882 ATCAATCAATAGCAAGATAA-GGCAATTCAA
1 ATCAATCAATAGCAAGATAATGGCAATTCAA
* *
9912 ATCAA-CAATTGAAAGATA
1 ATCAATCAATAGCAAGATA
9930 GAATAAGCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 24 0.57
30 18 0.43
ACGTcount: A:0.49, C:0.15, G:0.12, T:0.24
Consensus pattern (31 bp):
ATCAATCAATAGCAAGATAATGGCAATTCAA
Found at i:12136 original size:14 final size:15
Alignment explanation
Indices: 12125--12156 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12115 GAAAATATGC
12125 AAATGCAAATATACT
1 AAATGCAAATATACT
12140 AAATGCAAA-A-ACT
1 AAATGCAAATATACT
12153 AAAT
1 AAAT
12157 TCCAGCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 1 0.06
15 9 0.53
ACGTcount: A:0.59, C:0.12, G:0.06, T:0.22
Consensus pattern (15 bp):
AAATGCAAATATACT
Found at i:14116 original size:29 final size:30
Alignment explanation
Indices: 14041--14117 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 30
14031 TTTGACAGCG
**
14041 AGTGCAAACCCACACTCAAATACAATCCCA
1 AGTGCAAACCCACACTTGAATACAATCCCA
14071 AGTGCAAACCCACACTTGAAT-CAA-CCCA
1 AGTGCAAACCCACACTTGAATACAATCCCA
*
14099 AGTGCACAACCCGCACTTG
1 AGTGCA-AACCCACACTTG
14118 TAAAAACACA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 10 0.23
29 14 0.33
30 19 0.44
ACGTcount: A:0.38, C:0.36, G:0.12, T:0.14
Consensus pattern (30 bp):
AGTGCAAACCCACACTTGAATACAATCCCA
Found at i:22745 original size:20 final size:20
Alignment explanation
Indices: 22717--22757 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
22707 CTGGTAAAAG
22717 AAGGAGATAAGAAGAGAAGA
1 AAGGAGATAAGAAGAGAAGA
* *
22737 AAGGGGATAAGAATAGAAGA
1 AAGGAGATAAGAAGAGAAGA
22757 A
1 A
22758 GAAATCTGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.34, T:0.07
Consensus pattern (20 bp):
AAGGAGATAAGAAGAGAAGA
Found at i:28736 original size:27 final size:28
Alignment explanation
Indices: 28706--28780 Score: 116
Period size: 27 Copynumber: 2.7 Consensus size: 28
28696 AGGGTCACCT
28706 AGGGGCATTTTGGTCATTTTCACATTC-
1 AGGGGCATTTTGGTCATTTTCACATTCA
**
28733 AGGGGCATTTTGGTCATTTTTGCATTCA
1 AGGGGCATTTTGGTCATTTTCACATTCA
*
28761 AGGGGGATTTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
28781 GAGTCCATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.17, C:0.13, G:0.27, T:0.43
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTTCACATTCA
Found at i:33516 original size:18 final size:19
Alignment explanation
Indices: 33493--33532 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
33483 TTCTTGAAAT
33493 AATTCTTC-AATGATCTTC
1 AATTCTTCAAATGATCTTC
*
33511 AATTCTTCAAATTATCTTC
1 AATTCTTCAAATGATCTTC
33530 AAT
1 AAT
33533 AAATCTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.33, C:0.20, G:0.03, T:0.45
Consensus pattern (19 bp):
AATTCTTCAAATGATCTTC
Found at i:37985 original size:24 final size:24
Alignment explanation
Indices: 37957--38004 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
37947 TGGAACAGCC
37957 ACCTGGCTTTGAAGATAGCAAACA
1 ACCTGGCTTTGAAGATAGCAAACA
37981 ACCTGGCTTTGAAGATAGCAAACA
1 ACCTGGCTTTGAAGATAGCAAACA
38005 CCCTAACTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (24 bp):
ACCTGGCTTTGAAGATAGCAAACA
Found at i:39371 original size:22 final size:22
Alignment explanation
Indices: 39341--39385 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
39331 AGATTTACTT
*
39341 ACTCCTTCTTCTTCCCGAAAAA
1 ACTCCTTCTTCTTCCCAAAAAA
* *
39363 ACTCGTTCTTTTTCCCAAAAAA
1 ACTCCTTCTTCTTCCCAAAAAA
39385 A
1 A
39386 TCTTCTAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.04, T:0.33
Consensus pattern (22 bp):
ACTCCTTCTTCTTCCCAAAAAA
Found at i:44141 original size:39 final size:39
Alignment explanation
Indices: 44087--44174 Score: 131
Period size: 39 Copynumber: 2.3 Consensus size: 39
44077 CATCATATGC
44087 ATTAAGAAAACACAGTCAGTAAAGTCAAAATTCAGGGTA
1 ATTAAGAAAACACAGTCAGTAAAGTCAAAATTCAGGGTA
* * **
44126 ATTAAGAGAACACAGTCAGTAAGGTCTTAATTCAGGGTA
1 ATTAAGAAAACACAGTCAGTAAAGTCAAAATTCAGGGTA
*
44165 ATTAATAAAA
1 ATTAAGAAAA
44175 TCAATCAAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.24
Consensus pattern (39 bp):
ATTAAGAAAACACAGTCAGTAAAGTCAAAATTCAGGGTA
Found at i:44224 original size:36 final size:36
Alignment explanation
Indices: 44115--44442 Score: 332
Period size: 36 Copynumber: 9.1 Consensus size: 36
44105 GTAAAGTCAA
*
44115 AATTCAGGGTAATTAAG-AGAACA-CAGTCAGTAAGGTCTT
1 AATTCAGGGTAATTAAGTA-AA-AGCAGTCA--AA-GACTT
* * *
44154 AATTCAGGGTAATTAA-TAAAATCAATCAAGGACTT
1 AATTCAGGGTAATTAAGTAAAAGCAGTCAAAGACTT
* *
44189 AATTTAGGGTAATTAAGTAAAAGCAGTAAAAGACTT
1 AATTCAGGGTAATTAAGTAAAAGCAGTCAAAGACTT
44225 AATTCAGGGTAATTAAGTAAAAGCAGT-AAAGGACTT
1 AATTCAGGGTAATTAAGTAAAAGCAGTCAAA-GACTT
* * * *
44261 AATTCGGGGAAATTAAGTAAAAGTAGTTAAAGGACTT
1 AATTCAGGGTAATTAAGTAAAAGCAGTCAAA-GACTT
* *
44298 AATTCAGGGTAATTAAGTAAAAACAGGCAAAGACTT
1 AATTCAGGGTAATTAAGTAAAAGCAGTCAAAGACTT
* * *
44334 AGTTCAGGGTAATTAAGT-AAATCA-TCAAAGACTG
1 AATTCAGGGTAATTAAGTAAAAGCAGTCAAAGACTT
* * *
44368 AATTTAAGGG-AATTAAGTAAAACCAG-CACAGACTT
1 AA-TTCAGGGTAATTAAGTAAAAGCAGTCAAAGACTT
* *
44403 AATTCAGGGTAATTAAGTAAAACCAG-CACAGACTT
1 AATTCAGGGTAATTAAGTAAAAGCAGTCAAAGACTT
*
44438 GATTC
1 AATTC
44443 GCCAGCACAG
Statistics
Matches: 251, Mismatches: 29, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
34 23 0.09
35 76 0.30
36 93 0.37
37 35 0.14
38 7 0.03
39 17 0.07
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.26
Consensus pattern (36 bp):
AATTCAGGGTAATTAAGTAAAAGCAGTCAAAGACTT
Found at i:44299 original size:109 final size:108
Alignment explanation
Indices: 44115--44424 Score: 323
Period size: 109 Copynumber: 2.9 Consensus size: 108
44105 GTAAAGTCAA
* * *
44115 AATTCAGGGTAATTAAGAGAACACAGTCAGTAAGGTCTTAATTCAGGGTAATTAATAAAATCAAT
1 AATTCAGGGTAATTAAG-TAA-ACAGTCAGTAAGGACTTAATTCAGGGAAATTAATAAAATCAAT
* * * *
44180 CAAGGACTTAATTTAGGGTAATTAAGTAAAAGCAGTAAAAGACTT
64 AAAGGACTTAATTCAGGGTAATTAAGTAAAAACAGGAAAAGACTT
*
44225 AATTCAGGGTAATTAAGTAAA-AG-CAGTAAAGGACTTAATTCGGGGAAATTAAGTAAAAGT-AG
1 AATTCAGGGTAATTAAGTAAACAGTCAGT-AAGGACTTAATTCAGGGAAATTAA-TAAAA-TCA-
* *
44287 TTAAAGGACTTAATTCAGGGTAATTAAGTAAAAACAGGCAAAGACTT
62 ATAAAGGACTTAATTCAGGGTAATTAAGTAAAAACAGGAAAAGACTT
* * * * *
44334 AGTTCAGGGTAATTAAGTAAATCA-TCA--AA-GACTGAATTTAAGGG-AATTAAGTAAAACCAG
1 AATTCAGGGTAATTAAGTAAA-CAGTCAGTAAGGACTTAA-TTCAGGGAAATTAA-TAAAATCAA
* *
44394 CACA-GACTTAATTCAGGGTAATTAAGTAAAA
63 TAAAGGACTTAATTCAGGGTAATTAAGTAAAA
44425 CCAGCACAGA
Statistics
Matches: 173, Mismatches: 18, Indels: 23
0.81 0.08 0.11
Matches are distributed among these distances:
105 27 0.16
106 6 0.03
107 42 0.24
108 14 0.08
109 64 0.37
110 17 0.10
111 3 0.02
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.26
Consensus pattern (108 bp):
AATTCAGGGTAATTAAGTAAACAGTCAGTAAGGACTTAATTCAGGGAAATTAATAAAATCAATAA
AGGACTTAATTCAGGGTAATTAAGTAAAAACAGGAAAAGACTT
Found at i:44449 original size:19 final size:19
Alignment explanation
Indices: 44425--44462 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
44415 TTAAGTAAAA
44425 CCAGCACAGACTTGATTCG
1 CCAGCACAGACTTGATTCG
44444 CCAGCACAGACTTGATTCG
1 CCAGCACAGACTTGATTCG
44463 GGGTAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.32, G:0.21, T:0.21
Consensus pattern (19 bp):
CCAGCACAGACTTGATTCG
Found at i:44504 original size:36 final size:36
Alignment explanation
Indices: 44464--44606 Score: 168
Period size: 36 Copynumber: 3.9 Consensus size: 36
44454 CTTGATTCGG
*
44464 GGTAATTAAGTAAA-AGTAGTCAAAGACTTAATTCAA
1 GGTAATTAAGTAAACA-CAGTCAAAGACTTAATTCAA
* *
44500 GGTAATTAAGTAAACACAG-CAAAGACTTGATTCAG
1 GGTAATTAAGTAAACACAGTCAAAGACTTAATTCAA
*
44535 GGTAATTAAGTAAACACAGT-AAGAGACTTAATT-TA
1 GGTAATTAAGTAAACACAGTCAA-AGACTTAATTCAA
44570 GCGTAATTAAGTAAACACAGTTAACAAAGACTTAATT
1 G-GTAATTAAGTAAACACAG-T--CAAAGACTTAATT
44607 TCAATGAAGG
Statistics
Matches: 93, Mismatches: 6, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
35 36 0.39
36 43 0.46
37 2 0.02
39 10 0.11
40 2 0.02
ACGTcount: A:0.45, C:0.11, G:0.17, T:0.27
Consensus pattern (36 bp):
GGTAATTAAGTAAACACAGTCAAAGACTTAATTCAA
Found at i:44533 original size:35 final size:35
Alignment explanation
Indices: 44445--44589 Score: 159
Period size: 36 Copynumber: 4.1 Consensus size: 35
44435 CTTGATTCGC
* * **
44445 CAGCACAGACTTGATTCGGGGTAATTAAGTAAA-A
1 CAGCAAAGACTTAATTCAAGGTAATTAAGTAAACA
*
44479 GTAGTCAAAGACTTAATTCAAGGTAATTAAGTAAACA
1 -CAG-CAAAGACTTAATTCAAGGTAATTAAGTAAACA
* *
44516 CAGCAAAGACTTGATTCAGGGTAATTAAGTAAACA
1 CAGCAAAGACTTAATTCAAGGTAATTAAGTAAACA
* *
44551 CAGTAAGAGACTTAATT-TAGCGTAATTAAGTAAACA
1 CAGCAA-AGACTTAATTCAAG-GTAATTAAGTAAACA
44587 CAG
1 CAG
44590 TTAACAAAGA
Statistics
Matches: 94, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
35 38 0.40
36 55 0.59
37 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (35 bp):
CAGCAAAGACTTAATTCAAGGTAATTAAGTAAACA
Found at i:44562 original size:71 final size:71
Alignment explanation
Indices: 44445--44589 Score: 206
Period size: 71 Copynumber: 2.0 Consensus size: 71
44435 CTTGATTCGC
* * *
44445 CAGCACAGACTTGATTCGGGGTAATTAAGTAAAAGTAGTCAAAGACTTAATTCAAG-GTAATTAA
1 CAGCAAAGACTTGATTCAGGGTAATTAAGTAAAAGCAGTCAAAGACTTAATT-AAGCGTAATTAA
44509 GTAAACA
65 GTAAACA
*
44516 CAGCAAAGACTTGATTCAGGGTAATTAAGTAAACA-CAGT-AAGAGACTTAATTTAGCGTAATTA
1 CAGCAAAGACTTGATTCAGGGTAATTAAGTAAA-AGCAGTCAA-AGACTTAATTAAGCGTAATTA
44579 AGTAAACA
64 AGTAAACA
44587 CAG
1 CAG
44590 TTAACAAAGA
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
70 4 0.06
71 62 0.93
72 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (71 bp):
CAGCAAAGACTTGATTCAGGGTAATTAAGTAAAAGCAGTCAAAGACTTAATTAAGCGTAATTAAG
TAAACA
Found at i:44730 original size:41 final size:41
Alignment explanation
Indices: 44646--44858 Score: 300
Period size: 41 Copynumber: 5.2 Consensus size: 41
44636 ACAGAAATTA
* *
44646 GAAATTAGGTAAGGATAAGCACAGACTTAATTTTCAAGGAAG
1 GAAATTAGGTAAAGACAAGCACAGACTTAA-TTTCAAGGAAG
* * *
44688 GAAACTATGTAAAGACAAGTACAGACTTAATTTCAAGGAAG
1 GAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAG
* * *
44729 GAAATTAGGTAAGGATAAGCACAAACTTAATTTCAAGGAAG
1 GAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAG
*
44770 GAAATTAGGTAAAGACAAGTACAGACTTAATTTCAAGGAAG
1 GAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAG
* * * *
44811 GAAATTAGGTAAAGACAAGCATATACTTAATTTTAGGGAAG
1 GAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAG
44852 GAAATTA
1 GAAATTA
44859 AGTAGAGTCA
Statistics
Matches: 151, Mismatches: 20, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
41 126 0.83
42 25 0.17
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.23
Consensus pattern (41 bp):
GAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAG
Found at i:44733 original size:113 final size:116
Alignment explanation
Indices: 44597--44858 Score: 316
Period size: 123 Copynumber: 2.2 Consensus size: 116
44587 CAGTTAACAA
* *
44597 AGACTTAATTTCAATGAAGGAAATTAGGTAAGGATAAGCACAGA-AA-TT-A-GAAATTAGGTAA
1 AGACTTAATTTCAAGGAAGGAAATTAGGTAAGGATAAGCACAAATAATTTAAGGAAATTAGGTAA
* * * *
44658 GGATAAGCACAGACTTAATTTTCAAGGAAGGAAACTATGTAAAGACAAGTAC
66 AGACAAGCACAGACTTAA-TTTCAAGGAAGGAAACTAGGTAAAGACAAGCAC
44710 AGACTTAATTTCAAGGAAGGAAATTAGGTAAGGATAAGCACAAACTTAATTTCAAGGAAGGAAAT
1 AGACTTAATTTCAAGGAAGGAAATTAGGTAAGGATAAGCACAAA--TAATTT-----AAGGAAAT
* * *
44775 TAGGTAAAGACAAGTACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCAT
59 TAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAACTAGGTAAAGACAAGCAC
* * *
44833 ATACTTAATTTTAGGGAAGGAAATTA
1 AGACTTAATTTCAAGGAAGGAAATTA
44859 AGTAGAGTCA
Statistics
Matches: 126, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
113 42 0.33
116 2 0.02
117 2 0.02
123 53 0.42
124 27 0.21
ACGTcount: A:0.46, C:0.09, G:0.21, T:0.24
Consensus pattern (116 bp):
AGACTTAATTTCAAGGAAGGAAATTAGGTAAGGATAAGCACAAATAATTTAAGGAAATTAGGTAA
AGACAAGCACAGACTTAATTTCAAGGAAGGAAACTAGGTAAAGACAAGCAC
Found at i:44794 original size:82 final size:82
Alignment explanation
Indices: 44646--44858 Score: 336
Period size: 82 Copynumber: 2.6 Consensus size: 82
44636 ACAGAAATTA
* * *
44646 GAAATTAGGTAAGGATAAGCACAGACTTAATTTTCAAGGAAGGAAACTATGTAAAGACAAGTACA
1 GAAATTAGGTAAGGATAAGCACAAACTTAA-TTTCAAGGAAGGAAATTAGGTAAAGACAAGTACA
44711 GACTTAATTTCAAGGAAG
65 GACTTAATTTCAAGGAAG
44729 GAAATTAGGTAAGGATAAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGTACAG
1 GAAATTAGGTAAGGATAAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGTACAG
44794 ACTTAATTTCAAGGAAG
66 ACTTAATTTCAAGGAAG
* * * * * *
44811 GAAATTAGGTAAAGACAAGCATATACTTAATTTTAGGGAAGGAAATTA
1 GAAATTAGGTAAGGATAAGCACAAACTTAATTTCAAGGAAGGAAATTA
44859 AGTAGAGTCA
Statistics
Matches: 121, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
82 92 0.76
83 29 0.24
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.23
Consensus pattern (82 bp):
GAAATTAGGTAAGGATAAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGTACAG
ACTTAATTTCAAGGAAG
Found at i:45090 original size:36 final size:36
Alignment explanation
Indices: 44854--45083 Score: 239
Period size: 36 Copynumber: 6.6 Consensus size: 36
44844 TAGGGAAGGA
* *
44854 AATTAAGTAGAGTCAATAAAGGGCTTAATTCAGGGT
1 AATTAAGTGGAGTCAATAAAGAGCTTAATTCAGGGT
* *
44890 AATTAAGT--AG--AATAAAGAACTTAATTCAGGGA
1 AATTAAGTGGAGTCAATAAAGAGCTTAATTCAGGGT
*
44922 AATTAAGTGGAGTCAATAAA-AGGCTTAATTCAAGGT
1 AATTAAGTGGAGTCAATAAAGA-GCTTAATTCAGGGT
* * * * * *
44958 AATTGAGCAGAATTC-ATAAAGAACTTAATTTAGGGT
1 AATTAAG-TGGAGTCAATAAAGAGCTTAATTCAGGGT
44994 AATTAAGTGGAGTCAATAAA-AGGCTTAATTCAGGGT
1 AATTAAGTGGAGTCAATAAAGA-GCTTAATTCAGGGT
* *
45030 AATTAAGT--AG--AATAAAGAGCTTAATTCCGGGC
1 AATTAAGTGGAGTCAATAAAGAGCTTAATTCAGGGT
45062 AATTAAGTGGAGTCAATAAAGA
1 AATTAAGTGGAGTCAATAAAGA
45084 ATTTAATCTA
Statistics
Matches: 159, Mismatches: 21, Indels: 28
0.76 0.10 0.13
Matches are distributed among these distances:
32 53 0.33
33 1 0.01
34 8 0.05
35 6 0.04
36 86 0.54
37 5 0.03
ACGTcount: A:0.43, C:0.08, G:0.22, T:0.27
Consensus pattern (36 bp):
AATTAAGTGGAGTCAATAAAGAGCTTAATTCAGGGT
Found at i:45090 original size:68 final size:68
Alignment explanation
Indices: 44851--45081 Score: 336
Period size: 68 Copynumber: 3.3 Consensus size: 68
44841 TTTTAGGGAA
* *
44851 GGAAATTAAGTAGAGTCAATAAAGGGCTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATT
1 GGAAATTAAGTGGAGTCAATAAAAGGCTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATT
44916 CAG
66 CAG
* * *
44919 GGAAATTAAGTGGAGTCAATAAAAGGCTTAATTCAAGGTAATTGAGCAGAATTCATAAAGAACTT
1 GGAAATTAAGTGGAGTCAATAAAAGGCTTAATTCAGGGTAATTAAGTAG-A---ATAAAGAACTT
*
44984 AATTTAG
62 AATTCAG
* *
44991 GGTAATTAAGTGGAGTCAATAAAAGGCTTAATTCAGGGTAATTAAGTAGAATAAAGAGCTTAATT
1 GGAAATTAAGTGGAGTCAATAAAAGGCTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATT
*
45056 CCG
66 CAG
*
45059 GGCAATTAAGTGGAGTCAATAAA
1 GGAAATTAAGTGGAGTCAATAAA
45082 GAATTTAATC
Statistics
Matches: 145, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
68 81 0.56
69 1 0.01
71 1 0.01
72 62 0.43
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (68 bp):
GGAAATTAAGTGGAGTCAATAAAAGGCTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATT
CAG
Found at i:46019 original size:72 final size:72
Alignment explanation
Indices: 45932--46073 Score: 275
Period size: 72 Copynumber: 2.0 Consensus size: 72
45922 AAGGCCGGGC
45932 CATGCGATGGTGATGGCCGGGCATGTGGCCGGTCAAGTGCTTGGCCATGTGCGATTGGATCATGG
1 CATGCGATGGTGATGGCCGGGCATGTGGCCGGTCAAGTGCTTGGCCATGTGCGATTGGATCATGG
45997 CTTGGGG
66 CTTGGGG
*
46004 CATGTGATGGTGATGGCCGGGCATGTGGCCGGTCAAGTGCTTGGCCATGTGCGATTGGATCATGG
1 CATGCGATGGTGATGGCCGGGCATGTGGCCGGTCAAGTGCTTGGCCATGTGCGATTGGATCATGG
46069 CTTGG
66 CTTGG
46074 CCGGTCATAT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.14, C:0.19, G:0.41, T:0.26
Consensus pattern (72 bp):
CATGCGATGGTGATGGCCGGGCATGTGGCCGGTCAAGTGCTTGGCCATGTGCGATTGGATCATGG
CTTGGGG
Found at i:48994 original size:125 final size:125
Alignment explanation
Indices: 48772--49016 Score: 463
Period size: 125 Copynumber: 2.0 Consensus size: 125
48762 CCTATATAAA
*
48772 GGGACCAACCCCCTCTTTTAAACACAAGTTAAGTTTTCAATAAAGATTTTGAGGTTTATTCACCC
1 GGGACCAACCCCCTCTTGTAAACACAAGTTAAGTTTTCAATAAAGATTTTGAGGTTTATTCACCC
48837 AAATTGATTATCTTAGCTTCATTGTTCTAGTTTGAGCATACTTAGGGTTCTTCAAGATGT
66 AAATTGATTATCTTAGCTTCATTGTTCTAGTTTGAGCATACTTAGGGTTCTTCAAGATGT
* *
48897 GGGACCAATCCCCTCTTGTAAACACAGGTTAAGTTTTCAATAAAGATTTTGAGGTTTATTCACCC
1 GGGACCAACCCCCTCTTGTAAACACAAGTTAAGTTTTCAATAAAGATTTTGAGGTTTATTCACCC
48962 AAATTGATTATCTTAGCTTCATTGTTCTAGTTTGAGCATACTTAGGGTTCTTCAA
66 AAATTGATTATCTTAGCTTCATTGTTCTAGTTTGAGCATACTTAGGGTTCTTCAA
49017 TCTTGTAGAG
Statistics
Matches: 117, Mismatches: 3, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
125 117 1.00
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (125 bp):
GGGACCAACCCCCTCTTGTAAACACAAGTTAAGTTTTCAATAAAGATTTTGAGGTTTATTCACCC
AAATTGATTATCTTAGCTTCATTGTTCTAGTTTGAGCATACTTAGGGTTCTTCAAGATGT
Found at i:50974 original size:41 final size:41
Alignment explanation
Indices: 50847--50984 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 41
50837 CCCACTAACT
* * * *
50847 AAAGTCCTCAAACACATTCTTAACATAGAGGCATCCATGTC
1 AAAGTCCTCAAACACATTTTTAACACAGAGGCATCTATCTC
* * * * *
50888 AAAGTCCTCAAACACAATTATAACACAGGGGCAACTCTCTC
1 AAAGTCCTCAAACACATTTTTAACACAGAGGCATCTATCTC
*
50929 AAAGTCCTCAAGCACATTTTTAACACAGAGGCATCTATACT-
1 AAAGTCCTCAAACACATTTTTAACACAGAGGCATCTAT-CTC
50970 AAAGTCC-CTAAACAC
1 AAAGTCCTC-AAACAC
50985 GTGCAACACA
Statistics
Matches: 79, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
40 1 0.01
41 76 0.96
42 2 0.03
ACGTcount: A:0.38, C:0.28, G:0.12, T:0.22
Consensus pattern (41 bp):
AAAGTCCTCAAACACATTTTTAACACAGAGGCATCTATCTC
Found at i:53116 original size:29 final size:29
Alignment explanation
Indices: 53079--53154 Score: 125
Period size: 29 Copynumber: 2.6 Consensus size: 29
53069 TTTGTTAATT
*
53079 GCGTTTAGACGCCGCTATTTAGAATGGCG
1 GCGTCTAGACGCCGCTATTTAGAATGGCG
*
53108 GCGTCTAGACGCCGCTATTTAGATTGGCG
1 GCGTCTAGACGCCGCTATTTAGAATGGCG
*
53137 GCGTCTAGACGCCACTAT
1 GCGTCTAGACGCCGCTAT
53155 ATTAAAGTGT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.20, C:0.25, G:0.29, T:0.26
Consensus pattern (29 bp):
GCGTCTAGACGCCGCTATTTAGAATGGCG
Found at i:56162 original size:30 final size:29
Alignment explanation
Indices: 56090--56169 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 29
56080 ACAACAAAAG
*
56090 ATTTATGAACAAAACCCAGAATTTTCCCA
1 ATTTATGAACAAAACCTAGAATTTTCCCA
56119 A--TATCGCAACAAAACCTAGAA-TTTCCCAGA
1 ATTTAT-G-AACAAAACCTAGAATTTTCCC--A
56149 ATTTATGAACAAAACCTAGAA
1 ATTTATGAACAAAACCTAGAA
56170 CATAACACCA
Statistics
Matches: 44, Mismatches: 1, Indels: 11
0.79 0.02 0.20
Matches are distributed among these distances:
27 3 0.07
28 7 0.16
29 14 0.32
30 16 0.36
31 1 0.02
32 3 0.07
ACGTcount: A:0.45, C:0.23, G:0.09, T:0.24
Consensus pattern (29 bp):
ATTTATGAACAAAACCTAGAATTTTCCCA
Found at i:57315 original size:31 final size:30
Alignment explanation
Indices: 57280--57384 Score: 156
Period size: 31 Copynumber: 3.4 Consensus size: 30
57270 ATGCCTCCAT
* *
57280 TTAGCGGCGTCTGGTTTCCAAGCGTCGCAGA
1 TTAGCGGCGTCTGGTTT-CAAACGCCGCAGA
*
57311 TTAGCGGCGTCTGTATTTCAAACGCCGCAGA
1 TTAGCGGCGTCTG-GTTTCAAACGCCGCAGA
57342 TTAGCGGCGTCTGGATTTCAAACGCCGCAGA
1 TTAGCGGCGTCTGG-TTTCAAACGCCGCAGA
57373 TTAGCGGCGTCT
1 TTAGCGGCGTCT
57385 ATCGTCTAGA
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
31 65 0.96
32 3 0.04
ACGTcount: A:0.19, C:0.26, G:0.30, T:0.26
Consensus pattern (30 bp):
TTAGCGGCGTCTGGTTTCAAACGCCGCAGA
Found at i:57567 original size:31 final size:31
Alignment explanation
Indices: 57529--57589 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
57519 ATCTAAACGC
57529 CACTAAATAGCGGCGTCTGAATTTAAGACGT
1 CACTAAATAGCGGCGTCTGAATTTAAGACGT
57560 CACTAAATAGCGGCGTCTGAATTTAAGACG
1 CACTAAATAGCGGCGTCTGAATTTAAGACG
57590 CCGCTATCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (31 bp):
CACTAAATAGCGGCGTCTGAATTTAAGACGT
Found at i:59793 original size:21 final size:22
Alignment explanation
Indices: 59757--59797 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
59747 TTTAAATTTG
*
59757 CTGTCAGAATTATGTTTAATGA
1 CTGTCAGAACTATGTTTAATGA
59779 CTGTCA-AACTATGTTTAAT
1 CTGTCAGAACTATGTTTAAT
59798 TACTACAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (22 bp):
CTGTCAGAACTATGTTTAATGA
Found at i:64089 original size:21 final size:22
Alignment explanation
Indices: 64053--64098 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
64043 TTTAAATTTG
*
64053 CTGTCAGAATTATGTTTAATGA
1 CTGTCAGAACTATGTTTAATGA
*
64075 CTGTCAG-ACTATGTTTAATTA
1 CTGTCAGAACTATGTTTAATGA
64096 CTG
1 CTG
64099 CTTTAATCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.41
Consensus pattern (22 bp):
CTGTCAGAACTATGTTTAATGA
Found at i:65455 original size:46 final size:46
Alignment explanation
Indices: 65388--65483 Score: 192
Period size: 46 Copynumber: 2.1 Consensus size: 46
65378 CGTGCGGCTG
65388 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAATCAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAATCAAA
65434 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAATCAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAATCAAA
65480 TTTT
1 TTTT
65484 GTTGTGAAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (46 bp):
TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAATCAAA
Found at i:65622 original size:59 final size:57
Alignment explanation
Indices: 65518--65642 Score: 191
Period size: 59 Copynumber: 2.2 Consensus size: 57
65508 GCAATTGAGT
* * *
65518 AAAAT-TGAAGTATGTTAAAGACGAGAATAGAGAGACAATAGAATATGGAGAAGGAG
1 AAAATATGAAGTATGTAAAAGACGAGAATAGAGAGACAATAAAATATGGAGAAGAAG
65574 AAAATATGAAGTATGTAAAAGACAAGAGAATAGAGAGACAATAAAATATGGAGAAGAAG
1 AAAATATGAAGTATGTAAAAGAC--GAGAATAGAGAGACAATAAAATATGGAGAAGAAG
65633 -AAATATGAAG
1 AAAATATGAAG
65643 AATGGGAGAA
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
56 5 0.08
57 16 0.25
58 10 0.16
59 32 0.51
ACGTcount: A:0.54, C:0.03, G:0.26, T:0.17
Consensus pattern (57 bp):
AAAATATGAAGTATGTAAAAGACGAGAATAGAGAGACAATAAAATATGGAGAAGAAG
Found at i:66142 original size:20 final size:21
Alignment explanation
Indices: 66112--66151 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
66102 TCTCTCCCTA
*
66112 AATATATATATCATAGATAAT
1 AATATATATATCATACATAAT
66133 AATA-ATATATCATACATAA
1 AATATATATATCATACATAA
66152 AATTATTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (21 bp):
AATATATATATCATACATAAT
Found at i:67057 original size:30 final size:30
Alignment explanation
Indices: 67022--67086 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
67012 TATTTGATTT
*
67022 TATTAGAAATATTTA-TTAATATGAAATAAA
1 TATTAG-AATATTGATTTAATATGAAATAAA
*
67052 TATTAGAATATTGATTTAATATGCAATAAA
1 TATTAGAATATTGATTTAATATGAAATAAA
67082 TATTA
1 TATTA
67087 TTAGAAATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 7 0.22
30 25 0.78
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.42
Consensus pattern (30 bp):
TATTAGAATATTGATTTAATATGAAATAAA
Done.