Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003674.1 Hibiscus syriacus cultivar Beakdansim tig00007848_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: 403236
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:270677 original size:96 final size:95
Alignment explanation
Indices: 270476--270699 Score: 258
Period size: 96 Copynumber: 2.3 Consensus size: 95
270466 TGGCTCTATA
* * * * * * *
270476 GTATCGATACCCCTACCATCGTATCGATACTACTATATTATGGTATCGATATCCCCTTCTAGTAT
1 GTATCGATACCCTTACCATGGTATCGATACTACTATATTATAGTACCGATATACCCTACTAATAT
* **
270541 CGATACCAATTTTTGATTCGATGTTGCTTG
66 CGATACCAATTTTAGATTCGATGAAGCTTG
270571 GTATCGATACCCTTACCATGGTATCGATACTACTATATATTATAGTACCGATA-ACCCTAAC-AA
1 GTATCGATACCCTTACCATGGTATCGATACTAC--TATATTATAGTACCGATATACCCT-ACTAA
*
270634 TATCGATACTC-ATTTTAGTTTCGATGAAGAC-TG
63 TATCGATAC-CAATTTTAGATTCGATGAAG-CTTG
* *
270667 GTATCGATACCCTTACTATGGTATTGATACTAC
1 GTATCGATACCCTTACCATGGTATCGATACTAC
270700 CTAGTCGATA
Statistics
Matches: 111, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
95 31 0.28
96 61 0.55
97 19 0.17
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (95 bp):
GTATCGATACCCTTACCATGGTATCGATACTACTATATTATAGTACCGATATACCCTACTAATAT
CGATACCAATTTTAGATTCGATGAAGCTTG
Found at i:276288 original size:14 final size:13
Alignment explanation
Indices: 276256--276293 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
276246 ATTAATACTA
276256 ATAATATATA-AC
1 ATAATATATATAC
*
276268 TTAATATAGTATAC
1 ATAATATA-TATAC
276282 ATAATATATATA
1 ATAATATATATA
276294 TTGTATATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 7 0.32
13 6 0.27
14 9 0.41
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (13 bp):
ATAATATATATAC
Found at i:276340 original size:9 final size:9
Alignment explanation
Indices: 276271--276383 Score: 57
Period size: 9 Copynumber: 13.4 Consensus size: 9
276261 ATATAACTTA
*
276271 ATATAGTAT
1 ATATAATAT
*
276280 ACATAATAT
1 ATATAATAT
* *
276289 ATATATTGT
1 ATATAATAT
***
276298 ATATACGCT
1 ATATAATAT
*
276307 ATTTAATAT
1 ATATAATAT
*
276316 A-ATACTAT
1 ATATAATAT
276324 ACTA-AATAT
1 A-TATAATAT
276333 ATATAATAT
1 ATATAATAT
276342 ATAT--TAT
1 ATATAATAT
276349 A-A-AATAT
1 ATATAATAT
276356 ATA-AATACT
1 ATATAATA-T
276365 ATAT-A-AT
1 ATATAATAT
276372 -TATAATAT
1 ATATAATAT
276380 ATAT
1 ATAT
276384 TATACGTAAC
Statistics
Matches: 78, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
6 4 0.05
7 10 0.13
8 16 0.21
9 47 0.60
10 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (9 bp):
ATATAATAT
Found at i:276880 original size:22 final size:23
Alignment explanation
Indices: 276837--276882 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
276827 ATGAACATTG
*
276837 CTAAAGTTGTTGACATGGTACTATA
1 CTAAAGTTGTCGACA--GTACTATA
276862 CTAAAGTTGTCGACA-TACTAT
1 CTAAAGTTGTCGACAGTACTAT
276883 TTTATCAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 6 0.30
25 14 0.70
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (23 bp):
CTAAAGTTGTCGACAGTACTATA
Found at i:285559 original size:19 final size:20
Alignment explanation
Indices: 285517--285559 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
285507 CCCCTTGAAG
*
285517 GGGAACCGATTCCCTCCCAA
1 GGGAACCGATACCCTCCCAA
* *
285537 GGGAATCGATACCC-CCCAC
1 GGGAACCGATACCCTCCCAA
285556 GGGA
1 GGGA
285560 TCTGGATGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.12
Consensus pattern (20 bp):
GGGAACCGATACCCTCCCAA
Found at i:285938 original size:2 final size:2
Alignment explanation
Indices: 285931--285962 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
285921 CAAAATTAAA
285931 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
285963 TTTTGAGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:288049 original size:21 final size:20
Alignment explanation
Indices: 288025--288386 Score: 270
Period size: 21 Copynumber: 17.4 Consensus size: 20
288015 CATATTCGCA
*
288025 TTGCGA-TAGTCCAAGTTCGCG
1 TTGCGATTATTCCAAGTT--CG
*
288046 TTGCGATTTATTCCAAATTCG
1 TTGCGA-TTATTCCAAGTTCG
*
288067 TTGCGATTTATTCCAAATTCG
1 TTGCGA-TTATTCCAAGTTCG
*
288088 TTGCGATTTATTCCAAATTCG
1 TTGCGA-TTATTCCAAGTTCG
*
288109 TTGCGA-TAGTCCAAGTTCG
1 TTGCGATTATTCCAAGTTCG
288128 CATTGCGATTTATTCCAAGTTCG
1 --TTGCGA-TTATTCCAAGTTCG
* *
288151 TTGCGA-TAGTCGAAGTTCACG
1 TTGCGATTATTCCAAGTT--CG
*
288172 TTGCGATTTATTCCAAATTCG
1 TTGCGA-TTATTCCAAGTTCG
*
288193 TTGCGATTTATTCCAAATTCG
1 TTGCGA-TTATTCCAAGTTCG
* *
288214 TTGCGA-TAGTCCATGTTCGCG
1 TTGCGATTATTCCAAGTT--CG
*
288235 TTGCGATTTATTCTAAGTTCG
1 TTGCGA-TTATTCCAAGTTCG
* ** *
288256 TTGC-AATAGACAAAGTTCGCG
1 TTGCGATTATTCCAAGTT--CG
*
288277 TTGCGATTTATTCCAAATTCG
1 TTGCGA-TTATTCCAAGTTCG
*
288298 TTGCGATTTATTCCAAATTCG
1 TTGCGA-TTATTCCAAGTTCG
*
288319 TTGCGA-TAGTCCAAGTTCG
1 TTGCGATTATTCCAAGTTCG
* *
288338 TTGCGA-TAGTCGAAGTTCGCG
1 TTGCGATTATTCCAAGTT--CG
* *
288359 TTGCGATTTATTCCAAATTCT
1 TTGCGA-TTATTCCAAGTTCG
288380 TTGCGAT
1 TTGCGAT
288387 AGTCCAAAAT
Statistics
Matches: 287, Mismatches: 32, Indels: 45
0.79 0.09 0.12
Matches are distributed among these distances:
19 63 0.22
20 2 0.01
21 169 0.59
22 1 0.00
23 52 0.18
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
TTGCGATTATTCCAAGTTCG
Found at i:288090 original size:42 final size:42
Alignment explanation
Indices: 288044--288386 Score: 316
Period size: 42 Copynumber: 8.2 Consensus size: 42
288034 TCCAAGTTCG
288044 CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
* *
288086 CGTTGCGATTTATTCCAAATTCGTTGCGA--TAGTCCAAGTT
1 CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
* * * *
288126 CGCATTGCGATTTATTCCAAGTTCGTTGCGA--TAGTCGAAGTT
1 CG--TTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
288168 CACGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
1 --CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
* ** * *
288212 CGTTGCGA--TAGTCCATGTTCGCGTTGCGATTTATTCTAAGTT
1 CGTTGCGATTTATTCCAAATT--CGTTGCGATTTATTCCAAATT
* **
288254 CGTTGC-A-ATA-GACAAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAA-TT--CGTTGCGATTTATTCCAAATT
* *
288296 CGTTGCGATTTATTCCAAATTCGTTGCGA--TAGTCCAAGTT
1 CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
* * *
288336 CGTTGCGA--TAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATT--CGTTGCGATTTATTCCAAATT
*
288378 CTTTGCGAT
1 CGTTGCGAT
288387 AGTCCAAAAT
Statistics
Matches: 253, Mismatches: 30, Indels: 35
0.80 0.09 0.11
Matches are distributed among these distances:
38 8 0.03
40 44 0.17
41 3 0.01
42 179 0.71
43 1 0.00
44 14 0.06
45 4 0.02
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (42 bp):
CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
Found at i:288201 original size:105 final size:104
Alignment explanation
Indices: 288065--288344 Score: 481
Period size: 105 Copynumber: 2.7 Consensus size: 104
288055 ATTCCAAATT
288065 CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCA
1 CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGC-
* * *
288130 TTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCA
65 TTGCGATTTATTCCAAGTTCGTTGCAATAGACAAAGTTCA
*
288170 CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCATGTTCGCG
1 CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGC-
* *
288235 TTGCGATTTATTCTAAGTTCGTTGCAATAGACAAAGTTCG
65 TTGCGATTTATTCCAAGTTCGTTGCAATAGACAAAGTTCA
288275 CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG-T
1 CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCT
288339 TGCGAT
66 TGCGAT
288345 AGTCGAAGTT
Statistics
Matches: 167, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
103 7 0.04
105 160 0.96
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (104 bp):
CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCT
TGCGATTTATTCCAAGTTCGTTGCAATAGACAAAGTTCA
Found at i:288490 original size:6 final size:6
Alignment explanation
Indices: 288479--288509 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
288469 GACACGTATT
*
288479 ACCACG ACCACG ACCACG ACCATG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
288510 GATGAGACGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.35, C:0.45, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:289037 original size:6 final size:6
Alignment explanation
Indices: 289012--289064 Score: 85
Period size: 6 Copynumber: 9.3 Consensus size: 6
289002 CTCGTCTCGA
289012 GTCG-G GTCG-G GTCG-G GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
289057 GTCGTG GT
1 GTCGTG GT
289065 AATACGTGTC
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 14 0.30
6 33 0.70
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.30
Consensus pattern (6 bp):
GTCGTG
Found at i:289235 original size:40 final size:42
Alignment explanation
Indices: 289157--289249 Score: 163
Period size: 40 Copynumber: 2.3 Consensus size: 42
289147 TGCGATTTTG
289157 GACTATCGCAACGAATTTGGAATAAATCGAAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGAAACGCGAACTTC
*
289199 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGAAACGCGAACTTC
289239 GACTATCGCAA
1 GACTATCGCAA
289250 TGCAAATTTG
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 29 0.58
41 1 0.02
42 20 0.40
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGAAACGCGAACTTC
Found at i:289263 original size:21 final size:20
Alignment explanation
Indices: 289148--289266 Score: 89
Period size: 21 Copynumber: 5.8 Consensus size: 20
289138 ACCAGGCGTT
*
289148 GCGATTTTGGACTATCGCAA
1 GCGAATTTGGACTATCGCAA
* *
289168 -CGAATTTGGAATAAATCGAAA
1 GCGAATTTGGACT--ATCGCAA
* *
289189 CGCGAACTTCGACTATCGCAA
1 -GCGAATTTGGACTATCGCAA
**
289210 -CGAATTTGGAAAATCGCAA
1 GCGAATTTGGACTATCGCAA
* *
289229 CGCGAACTTCGACTATCGCAA
1 -GCGAATTTGGACTATCGCAA
*
289250 TGCAAATTTGGACTATC
1 -GCGAATTTGGACTATC
289267 TGGACTATCG
Statistics
Matches: 74, Mismatches: 19, Indels: 11
0.71 0.18 0.11
Matches are distributed among these distances:
19 25 0.34
21 40 0.54
23 9 0.12
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (20 bp):
GCGAATTTGGACTATCGCAA
Found at i:289395 original size:21 final size:21
Alignment explanation
Indices: 289342--289396 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
289332 AATTTGGAAA
* *
289342 ATCGCAACGCAAACTTTGACT
1 ATCGCAACGCGAACTTGGACT
289363 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
*
289384 ATCGCAATGCGAA
1 ATCGCAACGCGAA
289397 TATGTAAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:295305 original size:11 final size:12
Alignment explanation
Indices: 295274--295298 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
295264 GCATTCAGAT
295274 GAAATGCAATGA
1 GAAATGCAATGA
295286 GAAATGCAATGA
1 GAAATGCAATGA
295298 G
1 G
295299 GATGCAACAA
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:0.48, C:0.08, G:0.28, T:0.16
Consensus pattern (12 bp):
GAAATGCAATGA
Found at i:306210 original size:20 final size:20
Alignment explanation
Indices: 306185--306225 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
306175 GTCCTTGCTG
306185 CAAATGATGTCATCTTACTT
1 CAAATGATGTCATCTTACTT
*
306205 CAAATGATGTCATCTTGCTT
1 CAAATGATGTCATCTTACTT
306225 C
1 C
306226 GTTCTCTTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (20 bp):
CAAATGATGTCATCTTACTT
Found at i:307406 original size:24 final size:24
Alignment explanation
Indices: 307379--307451 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
307369 CGTTCATTTA
307379 CGTTCG-TGAACGTTCGGTTATGTT
1 CGTTCGAT-AACGTTCGGTTATGTT
* * *
307403 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGATAACGTTCGGTTATGTT
* * *
307427 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGATAACGTTCGGTTATGTT
307451 C
1 C
307452 TTTCATTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
24 44 0.98
25 1 0.02
ACGTcount: A:0.12, C:0.15, G:0.23, T:0.49
Consensus pattern (24 bp):
CGTTCGATAACGTTCGGTTATGTT
Found at i:307408 original size:14 final size:14
Alignment explanation
Indices: 307389--307444 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
307379 CGTTCGTGAA
*
307389 CGTTCGGTTATGTT
1 CGTTCGATTATGTT
307403 CGTTCGATTATGTT
1 CGTTCGATTATGTT
307417 CG-T---TTATGTT
1 CGTTCGATTATGTT
307427 CGTTCGATTATGTT
1 CGTTCGATTATGTT
307441 CGTT
1 CGTT
307445 TATGTTCTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.11, C:0.14, G:0.23, T:0.52
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:307461 original size:24 final size:24
Alignment explanation
Indices: 307390--307464 Score: 116
Period size: 24 Copynumber: 3.1 Consensus size: 24
307380 GTTCGTGAAC
*
307390 GTTCGGTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTCGATTAT
307414 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTCGATTAT
*
307438 GTTCGTTTATGTTCTTTC-ATTTAT
1 GTTCGTTTATGTTCGTTCGA-TTAT
307462 GTT
1 GTT
307465 TAACCCAATC
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
23 1 0.02
24 47 0.98
ACGTcount: A:0.12, C:0.12, G:0.20, T:0.56
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGATTAT
Found at i:308430 original size:10 final size:10
Alignment explanation
Indices: 308412--308486 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
308402 GGGTCTCCAA
*
308412 CGTTGATGTT
1 CGTTTATGTT
308422 CGTTTATGTT
1 CGTTTATGTT
308432 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* *
308443 ATGTTCATGTT
1 -CGTTTATGTT
308454 CGTTTATGTT
1 CGTTTATGTT
308464 CG----TGTT
1 CGTTTATGTT
308470 CGTTTATGTT
1 CGTTTATGTT
308480 CGTTTAT
1 CGTTTAT
308487 TTATTAAATG
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
6 6 0.12
10 35 0.67
11 7 0.13
12 4 0.08
ACGTcount: A:0.11, C:0.12, G:0.21, T:0.56
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:308443 original size:16 final size:16
Alignment explanation
Indices: 308418--308482 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
308408 CCAACGTTGA
308418 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
* *
308434 TGTTCATTTATGTTCA
1 TGTTCGTTTATGTTCG
308450 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
308466 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
308482 T
1 T
308483 TTATTTATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.09, C:0.12, G:0.22, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:308574 original size:16 final size:16
Alignment explanation
Indices: 308553--308595 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
308543 AAAAAAAATT
308553 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
308569 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
308585 TGTTCGTTTAT
1 TGTTCGTTTAT
308596 TAAATGAACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.07, C:0.12, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:315487 original size:6 final size:6
Alignment explanation
Indices: 315413--315489 Score: 91
Period size: 6 Copynumber: 12.8 Consensus size: 6
315403 TGTATACTCT
* * * * *
315413 CTAGCA CTGGCA CTGGCA CTGGCA CTAGCA CCAGGA CTAGCA CTAGCA
1 CTAGCA CTAGCA CTAGCA CTAGCA CTAGCA CTAGCA CTAGCA CTAGCA
* *
315461 CTAGCA CTGGCA CTGGCA CTAGCA CTAGC
1 CTAGCA CTAGCA CTAGCA CTAGCA CTAGC
315490 CGGAGCAGGT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 63 1.00
ACGTcount: A:0.26, C:0.34, G:0.25, T:0.16
Consensus pattern (6 bp):
CTAGCA
Found at i:315837 original size:24 final size:23
Alignment explanation
Indices: 315797--315841 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
315787 ATTAACATAT
*
315797 ATTTTTTAGATATTTTACTTTTAA
1 ATTTTTTAGATAATTTA-TTTTAA
315821 ATTTTATTA-ATAATTTATTTT
1 ATTTT-TTAGATAATTTATTTT
315842 CCTCTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 4 0.21
24 12 0.63
25 3 0.16
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (23 bp):
ATTTTTTAGATAATTTATTTTAA
Found at i:316557 original size:24 final size:24
Alignment explanation
Indices: 316525--316580 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
316515 CTATTCTTTC
*
316525 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAA
316549 GCTTCAATTGAGCTCAAATTTTAA
1 GCTTCAATTGAGCTCAAATTTTAA
316573 GCTTCAAT
1 GCTTCAAT
316581 CGAACTTCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAA
Found at i:320478 original size:21 final size:21
Alignment explanation
Indices: 320448--320545 Score: 169
Period size: 21 Copynumber: 4.7 Consensus size: 21
320438 ATACCATGAC
*
320448 AGGTATCGATACCCCCTTGGG
1 AGGTACCGATACCCCCTTGGG
320469 AGGTACCGATACCCCCTTGGG
1 AGGTACCGATACCCCCTTGGG
320490 AGGTACCGATACCCCCTTGGG
1 AGGTACCGATACCCCCTTGGG
* *
320511 AGGTACTGATACCCCCTTAGG
1 AGGTACCGATACCCCCTTGGG
320532 AGGTACCGATACCC
1 AGGTACCGATACCC
320546 TCAGTTTGCA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 73 1.00
ACGTcount: A:0.21, C:0.32, G:0.27, T:0.20
Consensus pattern (21 bp):
AGGTACCGATACCCCCTTGGG
Found at i:327952 original size:24 final size:23
Alignment explanation
Indices: 327920--327980 Score: 81
Period size: 21 Copynumber: 2.7 Consensus size: 23
327910 TACCCTACAG
327920 GGTACCGATACCCCTATGCAAAGA
1 GGTACCGATACCCCTATGCAAA-A
* *
327944 GGTACCGATA--CCTATTCCAAA
1 GGTACCGATACCCCTATGCAAAA
327965 GGTACCGATACCCCTA
1 GGTACCGATACCCCTA
327981 GTGTTGATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 11 0.33
22 8 0.24
23 4 0.12
24 10 0.30
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (23 bp):
GGTACCGATACCCCTATGCAAAA
Found at i:328725 original size:26 final size:26
Alignment explanation
Indices: 328694--328747 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
328684 AAAGCTTGCA
328694 CCAAAATTTTAATTGCCAATTCACCC
1 CCAAAATTTTAATTGCCAATTCACCC
328720 CCAAAATTTTAATTGCCAATTCACCC
1 CCAAAATTTTAATTGCCAATTCACCC
328746 CC
1 CC
328748 TCTTGGCTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.33, G:0.04, T:0.30
Consensus pattern (26 bp):
CCAAAATTTTAATTGCCAATTCACCC
Found at i:329184 original size:13 final size:13
Alignment explanation
Indices: 329168--329232 Score: 54
Period size: 13 Copynumber: 5.5 Consensus size: 13
329158 ATGTAGAAAT
*
329168 TAAATGAATATAA
1 TAAATAAATATAA
329181 TAAATAAATATAA
1 TAAATAAATATAA
329194 T-AAT-AAT-TAA
1 TAAATAAATATAA
329204 T-AAT--AT-TAA
1 TAAATAAATATAA
* *
329213 TTATTAAATATAA
1 TAAATAAATATAA
329226 TAAATAA
1 TAAATAA
329233 TTAAAATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
9 6 0.14
10 9 0.20
11 3 0.07
12 5 0.11
13 21 0.48
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (13 bp):
TAAATAAATATAA
Found at i:329198 original size:16 final size:16
Alignment explanation
Indices: 329177--329263 Score: 68
Period size: 16 Copynumber: 5.3 Consensus size: 16
329167 TTAAATGAAT
329177 ATAATAAATAAATATA
1 ATAATAAATAAATATA
*
329193 ATAAT-AATTAATAATA
1 ATAATAAATAAAT-ATA
* * *
329209 TTAATTATTAAATATA
1 ATAATAAATAAATATA
*
329225 ATAAATAATTAAAATATA
1 AT-AATAAAT-AAATATA
* *
329243 GTAATATATAAATATA
1 ATAATAAATAAATATA
*
329259 GTAAT
1 ATAAT
329264 TAAAATAGTT
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
15 6 0.10
16 28 0.48
17 16 0.28
18 8 0.14
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
ATAATAAATAAATATA
Found at i:331866 original size:55 final size:55
Alignment explanation
Indices: 331798--332524 Score: 879
Period size: 55 Copynumber: 13.2 Consensus size: 55
331788 AAACAAACAT
* * * *
331798 TATGTGTGTAAAACCACGAAATTAATCATGAGTTGATGAATAACCGTACACGTAC
1 TATGTGTGCAAAACCACGAAATTCATCATGAGTTGATGAATAACCGTACATGCAC
* * * * *
331853 TATGTGTGCAAAACTATGAAATTCATCATAATTTGATGAATAACCATACATGCAC
1 TATGTGTGCAAAACCACGAAATTCATCATGAGTTGATGAATAACCGTACATGCAC
** * *
331908 TATGTGTGCAAAACCATAAAATTTATCATGAGTTGATGAATAACCGTACAGGCAC
1 TATGTGTGCAAAACCACGAAATTCATCATGAGTTGATGAATAACCGTACATGCAC
* ** *
331963 TATGTTTGCAAAACCAC-AGAATTCATCATGAGTTGATGAATAACTATACATGAAC
1 TATGTGTGCAAAACCACGA-AATTCATCATGAGTTGATGAATAACCGTACATGCAC
* * * *
332018 TATATGTGCAAGACCACAAAATTCATCATGAGTTGATTAAATAACCGTACATGCAC
1 TATGTGTGCAAAACCACGAAATTCATCATGAGTTGA-TGAATAACCGTACATGCAC
* * * * *
332074 TATGTGTGCAAAACCACGGAATTCATCATGAGTTGATGAATAATCGCATAGGCAC
1 TATGTGTGCAAAACCACGAAATTCATCATGAGTTGATGAATAACCGTACATGCAC
* *
332129 TATGTGTGCAAAACCACGAAATTCATCATGAGTTGATGAATAACTGTACAAGCAC
1 TATGTGTGCAAAACCACGAAATTCATCATGAGTTGATGAATAACCGTACATGCAC
* * * * *
332184 TATGTGTGCAAAACCA-TAAATTTTATCATGAGTTGATGAATAATCGTATATACAC
1 TATGTGTGCAAAACCACGAAA-TTCATCATGAGTTGATGAATAACCGTACATGCAC
* *
332239 TATGTGTACAAAACCAC-ATAATTCATCATGAGTTGATGAATAACTGTACATGCAC
1 TATGTGTGCAAAACCACGA-AATTCATCATGAGTTGATGAATAACCGTACATGCAC
* * * *
332294 TATGTGTGCAAGACCACAAAATTCATCATGAGTTGAATAAATAACCGTACAGGCAC
1 TATGTGTGCAAAACCACGAAATTCATCATGAGTTG-ATGAATAACCGTACATGCAC
* * * *
332350 TATGTGTGTAAAACCAC-ATAATTCATCATGAGTTGATGAATAATCGTATAGGCAC
1 TATGTGTGCAAAACCACGA-AATTCATCATGAGTTGATGAATAACCGTACATGCAC
* * * *
332405 TATGTGTGCAAAACCATGGAATTCATCATGAGTTGATGAATAACCGCACAAGCAC
1 TATGTGTGCAAAACCACGAAATTCATCATGAGTTGATGAATAACCGTACATGCAC
* * * * *
332460 TATGTGTGCAAGACCACGGAACTCATCATGAGTTGATGAACT-ACCGTATAAGCAC
1 TATGTGTGCAAAACCACGAAATTCATCATGAGTTGATGAA-TAACCGTACATGCAC
*
332515 TACGTGTGCA
1 TATGTGTGCA
332525 TCTTAAGAAA
Statistics
Matches: 580, Mismatches: 81, Indels: 22
0.85 0.12 0.03
Matches are distributed among these distances:
54 4 0.01
55 476 0.82
56 100 0.17
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (55 bp):
TATGTGTGCAAAACCACGAAATTCATCATGAGTTGATGAATAACCGTACATGCAC
Found at i:332219 original size:221 final size:217
Alignment explanation
Indices: 331798--332524 Score: 845
Period size: 221 Copynumber: 3.3 Consensus size: 217
331788 AAACAAACAT
* * * * * * *
331798 TATGTGTGTAAAACCACGAAATTAATCATGAGTTGATGAATAACCGTACACGTACTATGTGTGCA
1 TATGTGTGCAAGACCACAAAATTCATCATGAGTTGATAAATAACCGTACATGCACTATGTGTGCA
* * * * * *
331863 AAACTATGAAATTCATCATAATTTGATGAATAAC-CATACATGCACTATGTGTGCAAAACCATAA
66 AAACCACGAAATTCATCATGAGTTGATGAATAACGCAT--AGGCACTATGTGTGCAAAACCA-CA
* * * *
331927 AATTTATCATGAGTTGATGAATAACCGTACAGGCACTATGTTTGCAAAACCACAGAATTCATCAT
128 AATTCATCATGAGTTGATGAATAACTGTACAGGCACTATGTGTGCAAAACCATA-AATTCATCAT
331992 GAGTTGATGAATAACTATACATGAAC
192 GAGTTGATGAATAACTATACATGAAC
*
332018 TATATGTGCAAGACCACAAAATTCATCATGAGTTGATTAAATAACCGTACATGCACTATGTGTGC
1 TATGTGTGCAAGACCACAAAATTCATCATGAGTTGA-TAAATAACCGTACATGCACTATGTGTGC
*
332083 AAAACCACGGAATTCATCATGAGTTGATGAATAATCGCATAGGCACTATGTGTGCAAAACCACGA
65 AAAACCACGAAATTCATCATGAGTTGATGAATAA-CGCATAGGCACTATGTGTGCAAAACCAC-A
* *
332148 AATTCATCATGAGTTGATGAATAACTGTACAAGCACTATGTGTGCAAAACCATAAATTTTATCAT
128 AATTCATCATGAGTTGATGAATAACTGTACAGGCACTATGTGTGCAAAACCATAAA-TTCATCAT
332213 GAGTTGATGAATAATCGTAT--AT-ACAC
192 GAGTTGATGAATAA-C-TATACATGA-AC
* * * * *
332239 TATGTGTACAAAACCACATAATTCATCATGAGTTGATGAATAACTGTACATGCACTATGTGTGCA
1 TATGTGTGCAAGACCACAAAATTCATCATGAGTTGATAAATAACCGTACATGCACTATGTGTGCA
* * * * * *
332304 AGACCACAAAATTCATCATGAGTTGAATAAATAACCGTACAGGCACTATGTGTGTAAAACCACAT
66 AAACCACGAAATTCATCATGAGTTG-ATGAATAA-CGCATAGGCACTATGTGTGCAAAACCACA-
* *
332369 AATTCATCATGAGTTGATGAATAA-TCGTATAGGCACTATGTGTGCAAAACCATGGAATTCATCA
128 AATTCATCATGAGTTGATGAATAACT-GTACAGGCACTATGTGTGCAAAACCAT-AAATTCATCA
*** * *
332433 TGAGTTGATGAATAACCGCACAAGCAC
191 TGAGTTGATGAATAACTATACATGAAC
** * * * * *
332460 TATGTGTGCAAGACCACGGAACTCATCATGAGTTGATGAACT-ACCGTATAAGCACTACGTGTGC
1 TATGTGTGCAAGACCACAAAATTCATCATGAGTTGAT-AAATAACCGTACATGCACTATGTGTGC
332524 A
65 A
332525 TCTTAAGAAA
Statistics
Matches: 436, Mismatches: 55, Indels: 31
0.84 0.11 0.06
Matches are distributed among these distances:
220 86 0.20
221 338 0.78
222 6 0.01
223 6 0.01
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (217 bp):
TATGTGTGCAAGACCACAAAATTCATCATGAGTTGATAAATAACCGTACATGCACTATGTGTGCA
AAACCACGAAATTCATCATGAGTTGATGAATAACGCATAGGCACTATGTGTGCAAAACCACAAAT
TCATCATGAGTTGATGAATAACTGTACAGGCACTATGTGTGCAAAACCATAAATTCATCATGAGT
TGATGAATAACTATACATGAAC
Found at i:332304 original size:276 final size:276
Alignment explanation
Indices: 331798--332507 Score: 1064
Period size: 276 Copynumber: 2.6 Consensus size: 276
331788 AAACAAACAT
* * * * *
331798 TATGTGTGTAAAACCACGAAATTAATCATGAGTTGATGAATAACCGTACACGTACTATGTGTGCA
1 TATGTGTGTAAAACCACGAAATTCATCATGAGTTGATGAATAATCGTATAGGCACTATGTGTGCA
* * * * *
331863 AAACTATGAAATTCATCATAATTTGATGAATAACCATACATGCACTATGTGTGCAAAACCATAAA
66 AAACCATGAAATTCATCATGAGTTGATGAATAACCGTACAAGCACTATGTGTGCAAAACCATAAA
* * *
331928 ATTTATCATGAGTTGATGAATAACCGTACAGGCACTATGTTTGCAAAACCACAGAATTCATCATG
131 ATTTATCATGAGTTGATGAATAACCGTACAGACACTATGTGTACAAAACCACAGAATTCATCATG
*
331993 AGTTGATGAATAACTATACATGAACTATATGTGCAAGACCACAAAATTCATCATGAGTTGATTAA
196 AGTTGATGAATAACTATACATGAACTATATGTGCAAGACCACAAAATTCATCATGAGTTGAATAA
*
332058 ATAACCGTACATGCAC
261 ATAACCGTACAGGCAC
* * *
332074 TATGTGTGCAAAACCACGGAATTCATCATGAGTTGATGAATAATCGCATAGGCACTATGTGTGCA
1 TATGTGTGTAAAACCACGAAATTCATCATGAGTTGATGAATAATCGTATAGGCACTATGTGTGCA
* *
332139 AAACCACGAAATTCATCATGAGTTGATGAATAACTGTACAAGCACTATGTGTGCAAAACCATAAA
66 AAACCATGAAATTCATCATGAGTTGATGAATAACCGTACAAGCACTATGTGTGCAAAACCATAAA
* * * * *
332204 TTTTATCATGAGTTGATGAATAATCGTATATACACTATGTGTACAAAACCACATAATTCATCATG
131 ATTTATCATGAGTTGATGAATAACCGTACAGACACTATGTGTACAAAACCACAGAATTCATCATG
* * *
332269 AGTTGATGAATAACTGTACATGCACTATGTGTGCAAGACCACAAAATTCATCATGAGTTGAATAA
196 AGTTGATGAATAACTATACATGAACTATATGTGCAAGACCACAAAATTCATCATGAGTTGAATAA
332334 ATAACCGTACAGGCAC
261 ATAACCGTACAGGCAC
332350 TATGTGTGTAAAACCAC-ATAATTCATCATGAGTTGATGAATAATCGTATAGGCACTATGTGTGC
1 TATGTGTGTAAAACCACGA-AATTCATCATGAGTTGATGAATAATCGTATAGGCACTATGTGTGC
* * * ***
332414 AAAACCATGGAATTCATCATGAGTTGATGAATAACCGCACAAGCACTATGTGTGCAAGACCACGG
65 AAAACCATGAAATTCATCATGAGTTGATGAATAACCGTACAAGCACTATGTGTGCAAAACCATAA
* *
332479 AACTCATCATGAGTTGATGAACT-ACCGTA
130 AATTTATCATGAGTTGATGAA-TAACCGTA
332508 TAAGCACTAC
Statistics
Matches: 389, Mismatches: 43, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
276 388 1.00
277 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (276 bp):
TATGTGTGTAAAACCACGAAATTCATCATGAGTTGATGAATAATCGTATAGGCACTATGTGTGCA
AAACCATGAAATTCATCATGAGTTGATGAATAACCGTACAAGCACTATGTGTGCAAAACCATAAA
ATTTATCATGAGTTGATGAATAACCGTACAGACACTATGTGTACAAAACCACAGAATTCATCATG
AGTTGATGAATAACTATACATGAACTATATGTGCAAGACCACAAAATTCATCATGAGTTGAATAA
ATAACCGTACAGGCAC
Found at i:332752 original size:29 final size:29
Alignment explanation
Indices: 332700--332757 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
332690 TATATCAGCT
* * * * *
332700 AGATGAATGGTTAAATACTGTTGAGTAAA
1 AGATGAAAGGTCAAACACTATTGAATAAA
332729 AGATGAAAGGTCAAACACTATTGAATAAA
1 AGATGAAAGGTCAAACACTATTGAATAAA
332758 GGAATAATGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.26
Consensus pattern (29 bp):
AGATGAAAGGTCAAACACTATTGAATAAA
Found at i:338451 original size:55 final size:55
Alignment explanation
Indices: 337849--338426 Score: 721
Period size: 55 Copynumber: 10.5 Consensus size: 55
337839 AGGTTACATT
* * * *
337849 CCACAGAATTCATCATGAGTTGATAAATAATCGTACAGGCACTAAGTATGCAAAA
1 CCACAGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAAA
* * * * *
337904 CCACGGAATTCATCATGAGTTGATGGATAACCATTCAGGCACTATGTGTGCAACA
1 CCACAGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAAA
* * * * * *
337959 CCACAAAATTCATCCTGAGTTGATGAATAAACATACAAGCACTATGTGTACAAAA
1 CCACAGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAAA
* * **
338014 CCACGGAATTCATCATGAGTTGATGAATAACCGTACAGACACTATGTACGCAAAA
1 CCACAGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAAA
* **
338069 CCAC-GTAATTCATCATGAGTTGATGAATAACCGTATAGGCACTATGTGTTTAAAA
1 CCACAG-AATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAAA
* * *
338124 CCACAAAATTCATCATGAGTTGATGAATAATCGTACAGGCACTATGTGTGCAAGA
1 CCACAGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAAA
* * * * *
338179 CCAC-GTAATTCATCACGAGTTGATGAATAACAGGACATGCACTATGTGTCCAAAA
1 CCACAG-AATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAAA
* * ** **
338234 CCATATAATTCATCATGAGTTGATGAATAATTTGTACAAACACTATGTGTGCAAAA
1 CCACAGAATTCATCATGAGTTGATGAATAA-CCGTACAGGCACTATGTGTGCAAAA
* * * * *
338290 CCACAAAATTCATCATGAGTTGATGAATAACCATACATGCACTATGTATGCAAGA
1 CCACAGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAAA
*
338345 CCAC-GAAATTCATCATGAGTTGATGAATAACCGTACATGCACTATGTGTGCAAAA
1 CCACAG-AATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAAA
338400 CCACAGAATTCATCATGAGTTGATGAA
1 CCACAGAATTCATCATGAGTTGATGAA
338427 CTATCGTATA
Statistics
Matches: 446, Mismatches: 70, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
54 1 0.00
55 397 0.89
56 48 0.11
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (55 bp):
CCACAGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAAA
Found at i:345535 original size:29 final size:30
Alignment explanation
Indices: 345490--345550 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
345480 ATTTTGAGTT
* *
345490 ACGAAATGAAACGTTAGACACCAAATTGGA
1 ACGAAATGAAACATTAGACACCAAAATGGA
* *
345520 ACGAAAT-AAACATTAGGCACTAAAATGGA
1 ACGAAATGAAACATTAGACACCAAAATGGA
345549 AC
1 AC
345551 AAAAGGCATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.49, C:0.16, G:0.18, T:0.16
Consensus pattern (30 bp):
ACGAAATGAAACATTAGACACCAAAATGGA
Found at i:348492 original size:18 final size:18
Alignment explanation
Indices: 348469--348516 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
348459 TAAAGAGAGT
348469 AGTATCGATACCCCTATG
1 AGTATCGATACCCCTATG
348487 AGTATCGATACCCCTATG
1 AGTATCGATACCCCTATG
*
348505 AGTATCGGTACC
1 AGTATCGATACC
348517 AAAAATGCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (18 bp):
AGTATCGATACCCCTATG
Found at i:355772 original size:2 final size:2
Alignment explanation
Indices: 355765--355902 Score: 151
Period size: 2 Copynumber: 70.0 Consensus size: 2
355755 ATTATAATAC
355765 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
355807 AT AT AT AT AT AT AC AA AT -T AT -T CAT GT TT GCT -T TT GAT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT -AT AT AT -AT AT
*
355846 AA AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
355887 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
355903 TTCTTTCATA
Statistics
Matches: 120, Mismatches: 8, Indels: 16
0.83 0.06 0.11
Matches are distributed among these distances:
1 5 0.04
2 112 0.93
3 3 0.03
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:375331 original size:14 final size:13
Alignment explanation
Indices: 375297--375331 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
375287 AAATTTTGAA
*
375297 AAAACTATGTTTG
1 AAAACAATGTTTG
375310 AAAACAATGTTTG
1 AAAACAATGTTTG
375323 AAAATCAAT
1 AAAA-CAAT
375332 ATATAGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (13 bp):
AAAACAATGTTTG
Found at i:397393 original size:23 final size:23
Alignment explanation
Indices: 397363--397438 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 23
397353 GCATGTCCTT
397363 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
* ** *
397386 GTGCATCGGTGCACCCTC-ATG-
1 GTGCATCGATGCACATTCAAGGA
* *
397407 GTGTATCGATGCATATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
397430 -TGCATCGAT
1 GTGCATCGAT
397439 ACACTTAACA
Statistics
Matches: 40, Mismatches: 11, Indels: 5
0.71 0.20 0.09
Matches are distributed among these distances:
21 13 0.32
22 12 0.30
23 15 0.38
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.26
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGA
Done.