Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005595.1 Hibiscus syriacus cultivar Beakdansim tig00013018_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: 146505
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:1345 original size:63 final size:63
Alignment explanation
Indices: 1224--1402 Score: 270
Period size: 63 Copynumber: 2.8 Consensus size: 63
1214 GTCCTTGTTT
* *
1224 CATTGCATTTCAAAGG-TCATCAATTTTTACATCTGCATTTTGCATTTTCGCATTCTGCATAATG
1 CATTGCATGTCAAAGGATCATCAA-TTTTACATCTGTA-TTTGCATTTTCGCATTCTGCATAATG
*
1288 CATTGCATGTCAAAGGATCATCAATTTTGCATCTGTATTTGCATTTTCGCATTCTGCATAATG
1 CATTGCATGTCAAAGGATCATCAATTTTACATCTGTATTTGCATTTTCGCATTCTGCATAATG
* * * *
1351 CATTGCATGTCAAAGGATCATCACTTTTATATATGTATTTGCATGTTCGCAT
1 CATTGCATGTCAAAGGATCATCAATTTTACATCTGTATTTGCATTTTCGCAT
1403 GATCATCATA
Statistics
Matches: 106, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
63 73 0.69
64 26 0.25
65 7 0.07
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.41
Consensus pattern (63 bp):
CATTGCATGTCAAAGGATCATCAATTTTACATCTGTATTTGCATTTTCGCATTCTGCATAATG
Found at i:5907 original size:32 final size:31
Alignment explanation
Indices: 5864--5983 Score: 168
Period size: 32 Copynumber: 3.8 Consensus size: 31
5854 AAACAATAGA
5864 GGGCATCTTTGAAGATTCAACATCAAATGTT
1 GGGCATCTTTGAAGATTCAACATCAAATGTT
5895 GGTGCATCTTTGAAGATTCAACATCAAATGTT
1 GG-GCATCTTTGAAGATTCAACATCAAATGTT
* * *
5927 AGGGCATATTTGGAGATTCAACATCAAATATT
1 -GGGCATCTTTGAAGATTCAACATCAAATGTT
**
5959 GGGGCATCTTTGGGGATTCAACATC
1 -GGGCATCTTTGAAGATTCAACATC
5984 TGATGCGAAC
Statistics
Matches: 81, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
31 2 0.02
32 77 0.95
33 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.32
Consensus pattern (31 bp):
GGGCATCTTTGAAGATTCAACATCAAATGTT
Found at i:5966 original size:64 final size:64
Alignment explanation
Indices: 5863--5983 Score: 188
Period size: 64 Copynumber: 1.9 Consensus size: 64
5853 GAAACAATAG
* * *
5863 AGGGCATCTTTGAAGATTCAACATCAAATGTTGGTGCATCTTTGAAGATTCAACATCAAATGTT
1 AGGGCATATTTGAAGATTCAACATCAAATATTGGGGCATCTTTGAAGATTCAACATCAAATGTT
* **
5927 AGGGCATATTTGGAGATTCAACATCAAATATTGGGGCATCTTTGGGGATTCAACATC
1 AGGGCATATTTGAAGATTCAACATCAAATATTGGGGCATCTTTGAAGATTCAACATC
5984 TGATGCGAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 51 1.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.31
Consensus pattern (64 bp):
AGGGCATATTTGAAGATTCAACATCAAATATTGGGGCATCTTTGAAGATTCAACATCAAATGTT
Found at i:6686 original size:84 final size:83
Alignment explanation
Indices: 6508--6741 Score: 263
Period size: 84 Copynumber: 2.8 Consensus size: 83
6498 AGGAACTATT
* * * * *
6508 TACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAAACCTTCAAGCTCGACTACACTCA
1 TACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACC-AAACCTTCAAGTTCGA-TTCATTCA
*
6573 GCTCAAAAGCATACCAAATT
64 GCTCAAAAGCATACCAAATC
* *
6593 TACAGCATAACTCAAGGTGATAAGGGTTATCTGTCAACCAAACCTTCAAGTTCGATTCTATTCAG
1 TACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAACCTTCAAGTTCGATTC-ATTCAG
* **
6658 CTC-AAGGACATGTCAAATC
65 CTCAAAAG-CATACCAAATC
* * * * *
6677 TACAACATAACTCAAGGCGAGAAGGGTTATCCGTCAACGAACACCTTCGAGTTTGATTCCATTCA
1 TACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAA-ACCTTCAAGTTCGATT-CATTCA
6742 ACACGATGAC
Statistics
Matches: 127, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
83 5 0.04
84 67 0.53
85 54 0.43
86 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (83 bp):
TACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAACCTTCAAGTTCGATTCATTCAGC
TCAAAAGCATACCAAATC
Found at i:7346 original size:182 final size:182
Alignment explanation
Indices: 7039--7780 Score: 1027
Period size: 182 Copynumber: 4.0 Consensus size: 182
7029 TTATCTCTTG
* *
7039 ATTGACCCGATTTCCTCATCACGAAGGAACAGA-TTCATAATCGAAAATGACCCGATCTCTTCAT
1 ATTGACCCGATTTCCTCATCACGAAGGAACA-ACGTCATAATCGAAAATAACCCGATCTCTTCAT
* *
7103 CGCGGATGAGCAGTGTCGTCTTCAACATCAAATCGACCAGATCTCCTCATCACGAAGGAGCAGCG
65 CGCGGATGAGCAGTGTCGTCTTCAACATCAAACCGACCAGATCTCCTCATCACGAAGGAGCAGTG
* * * *
7168 TCACCCTCAGACAATCAAACTTTCTCATCACGAAGGAAACATATTATCCTCAA
130 TCACCCTCAGACAATCAAACTTCCTCATCACGAAGGAACCGTATTGTCCTCAA
* * * * * *
7221 ATTGACCTGATTCCCTCATCAAGAAGAAACAACGTCATAATTGAAAATAACCCGATCTCTTTATC
1 ATTGACCCGATTTCCTCATCACGAAGGAACAACGTCATAATCGAAAATAACCCGATCTCTTCATC
* *
7286 GCGGATGAGCAGTATCGTCTTCAACATCAAACCGACCCGATCTCCTCATCACGAAGGAGCAGTGT
66 GCGGATGAGCAGTGTCGTCTTCAACATCAAACCGACCAGATCTCCTCATCACGAAGGAGCAGTGT
* * *
7351 CACCCTCAGACAATCAGACTTCCTCATCACGAAGGAACCGTATTGTCCCCAG
131 CACCCTCAGACAATCAAACTTCCTCATCACGAAGGAACCGTATTGTCCTCAA
* * * **
7403 ATTGGCCCGAATTCCTCATCACGAAGGAACAACCTCATAATAAAAAATAACCCGATCTCTTCATC
1 ATTGACCCGATTTCCTCATCACGAAGGAACAACGTCATAATCGAAAATAACCCGATCTCTTCATC
* * * *
7468 GCAGATGAGCAGTGTCGTCTTCAACATCAAACCGACCCGATCTCCTAATCACGAAGGAGCAATGT
66 GCGGATGAGCAGTGTCGTCTTCAACATCAAACCGACCAGATCTCCTCATCACGAAGGAGCAGTGT
* *
7533 CACCCTCAAACAATCAAACTTCCTCATCACGAAAGAACCGTATTGTCCTCAAA
131 CACCCTCAGACAATCAAACTTCCTCATCACGAAGGAACCGTATTGTCCTC-AA
* *
7586 TTATCTCTTGACTGACCCGATTTCCTCATCACGAAGGAACATCGTCATAATCGAAAATGACCCGA
1 --A-----T---TGACCCGATTTCCTCATCACGAAGGAACAACGTCATAATCGAAAATAACCCGA
7651 TCTCTTCATCGCGGATGAGCAGTGTCGTCTTCAACATCAAACCGACCAGATCTCCTCATCACGAA
56 TCTCTTCATCGCGGATGAGCAGTGTCGTCTTCAACATCAAACCGACCAGATCTCCTCATCACGAA
* * ** * *
7716 GGAGCAGTGTCACCCTCAGGCAATCAGACTTCCTCATCATAAAGGAACCGTATTGCCCCCAA
121 GGAGCAGTGTCACCCTCAGACAATCAAACTTCCTCATCACGAAGGAACCGTATTGTCCTCAA
7778 ATT
1 ATT
7781 ATCTCTTGAT
Statistics
Matches: 491, Mismatches: 57, Indels: 24
0.86 0.10 0.04
Matches are distributed among these distances:
181 1 0.00
182 324 0.66
183 1 0.00
185 2 0.00
190 2 0.00
192 2 0.00
193 159 0.32
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.23
Consensus pattern (182 bp):
ATTGACCCGATTTCCTCATCACGAAGGAACAACGTCATAATCGAAAATAACCCGATCTCTTCATC
GCGGATGAGCAGTGTCGTCTTCAACATCAAACCGACCAGATCTCCTCATCACGAAGGAGCAGTGT
CACCCTCAGACAATCAAACTTCCTCATCACGAAGGAACCGTATTGTCCTCAA
Found at i:7681 original size:375 final size:365
Alignment explanation
Indices: 6937--7776 Score: 1144
Period size: 375 Copynumber: 2.2 Consensus size: 365
6927 AGTTGAATTT
* * * *
6937 TCAAACCGACCAGATCTCCTCATCACGAAAGAGCAGTGTCACTCTCAGATAATCAGACTTCCTAA
1 TCAAACCGACCAGATCTCCTCATCACGAAGGAGCAGTGTCACCCTCAGACAATCAGACTTCCTCA
*
7002 TCACGAAGGAACCGTATTGTCCCCAAATTATCTCTTGATTGACCCGATTTCCTCATCACGAAGGA
66 TCACGAAGGAACCGTATTGTCCCC-----A-----TGATTGACCCGAATTCCTCATCACGAAGGA
* ** * *
7067 ACAGATTCATAATCGAAAATGACCCGATCTCTTCATCGCGGATGAGCAGTGTCGTCTTCAACATC
121 ACAGACTCATAATAAAAAATAACCCGATCTCTTCATCGCAGATGAGCAGTGTCGTCTTCAACATC
* * * * *
7132 AAATCGACCAGATCTCCTCATCACGAAGGAGCAGCGTCACCCTCAGACAATCAAACTTTCTCATC
186 AAACCGACCAGATCTCCTAATCACGAAGGAGCAACGTCACCCTCAAACAATCAAACTTCCTCATC
* *
7197 ACGAAGGAAACATATTATCCTCAAATTGACCTGATTCCCTCATCAAGAAGAAACAACGTCATAAT
251 ACGAAAGAAACATATTATCCTCAAATTGACCCGATTCCCTCATCAAGAAGAAACAACGTCATAAT
* *
7262 TGAAAATAACCCGATCTCTTTATCGCGGATGAGCAGTATCGTCTTCAACA
316 CGAAAATAACCCGATCTCTTCATCGCGGATGAGCAGTATCGTCTTCAACA
*
7312 TCAAACCGACCCGATCTCCTCATCACGAAGGAGCAGTGTCACCCTCAGACAATCAGACTTCCTCA
1 TCAAACCGACCAGATCTCCTCATCACGAAGGAGCAGTGTCACCCTCAGACAATCAGACTTCCTCA
*
7377 TCACGAAGGAACCGTATTGTCCCCA-GATTGGCCCGAATTCCTCATCACGAAGGAACA-ACCTCA
66 TCACGAAGGAACCGTATTGTCCCCATGATTGACCCGAATTCCTCATCACGAAGGAACAGA-CTCA
7440 TAATAAAAAATAACCCGATCTCTTCATCGCAGATGAGCAGTGTCGTCTTCAACATCAAACCGACC
130 TAATAAAAAATAACCCGATCTCTTCATCGCAGATGAGCAGTGTCGTCTTCAACATCAAACCGACC
* *
7505 CGATCTCCTAATCACGAAGGAGCAATGTCACCCTCAAACAATCAAACTTCCTCATCACGAAAGAA
195 AGATCTCCTAATCACGAAGGAGCAACGTCACCCTCAAACAATCAAACTTCCTCATCACGAAAGAA
* * * * * * *
7570 CCGTATTGTCCTCAAATTATCTCTTGACTGACCCGATTTCCTCATCACGAAGGAACATCGTCATA
260 ACATATTATCCTC-AA--A-----T---TGACCCGATTCCCTCATCAAGAAGAAACAACGTCATA
* *
7635 ATCGAAAATGACCCGATCTCTTCATCGCGGATGAGCAGTGTCGTCTTCAACA
314 ATCGAAAATAACCCGATCTCTTCATCGCGGATGAGCAGTATCGTCTTCAACA
*
7687 TCAAACCGACCAGATCTCCTCATCACGAAGGAGCAGTGTCACCCTCAGGCAATCAGACTTCCTCA
1 TCAAACCGACCAGATCTCCTCATCACGAAGGAGCAGTGTCACCCTCAGACAATCAGACTTCCTCA
** *
7752 TCATAAAGGAACCGTATTGCCCCCA
66 TCACGAAGGAACCGTATTGTCCCCA
7777 AATTATCTCT
Statistics
Matches: 416, Mismatches: 37, Indels: 24
0.87 0.08 0.05
Matches are distributed among these distances:
363 1 0.00
364 161 0.39
365 2 0.00
367 1 0.00
370 1 0.00
372 1 0.00
375 249 0.60
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.23
Consensus pattern (365 bp):
TCAAACCGACCAGATCTCCTCATCACGAAGGAGCAGTGTCACCCTCAGACAATCAGACTTCCTCA
TCACGAAGGAACCGTATTGTCCCCATGATTGACCCGAATTCCTCATCACGAAGGAACAGACTCAT
AATAAAAAATAACCCGATCTCTTCATCGCAGATGAGCAGTGTCGTCTTCAACATCAAACCGACCA
GATCTCCTAATCACGAAGGAGCAACGTCACCCTCAAACAATCAAACTTCCTCATCACGAAAGAAA
CATATTATCCTCAAATTGACCCGATTCCCTCATCAAGAAGAAACAACGTCATAATCGAAAATAAC
CCGATCTCTTCATCGCGGATGAGCAGTATCGTCTTCAACA
Found at i:7749 original size:193 final size:193
Alignment explanation
Indices: 7408--7823 Score: 654
Period size: 193 Copynumber: 2.2 Consensus size: 193
7398 CCCAGATTGG
* * *
7408 CCCGAATTCCTCATCACGAAGGAACAACCTCATAATAAAAAATAACCCGATCTCTTCATCGCAGA
1 CCCGATTTCCTCATCACGAAGGAACATCGTCATAATAAAAAATAACCCGATCTCTTCATCGCAGA
*
7473 TGAGCAGTGTCGTCTTCAACATCAAACCGACCCGATCTCCTAATCACGAAGGAGCAATGTCACCC
66 TGAGCAGTGTCGTCTTCAACATCAAACCGACCAGATCTCCTAATCACGAAGGAGCAATGTCACCC
* *
7538 TCAAACAATCAAACTTCCTCATCACGAAA-GAACCGTATTGTCCTCAAATTATCTCTTGACTGA
131 TCAAACAATCAAACTTCCTCATCA-GAAAGGAACCGTATTGCCCCCAAATTATCTCTTGACTGA
** * *
7601 CCCGATTTCCTCATCACGAAGGAACATCGTCATAATCGAAAATGACCCGATCTCTTCATCGCGGA
1 CCCGATTTCCTCATCACGAAGGAACATCGTCATAATAAAAAATAACCCGATCTCTTCATCGCAGA
* *
7666 TGAGCAGTGTCGTCTTCAACATCAAACCGACCAGATCTCCTCATCACGAAGGAGCAGTGTCACCC
66 TGAGCAGTGTCGTCTTCAACATCAAACCGACCAGATCTCCTAATCACGAAGGAGCAATGTCACCC
** * * *
7731 TCAGGCAATCAGACTTCCTCATCATAAAGGAACCGTATTGCCCCCAAATTATCTCTTGATTGA
131 TCAAACAATCAAACTTCCTCATCAGAAAGGAACCGTATTGCCCCCAAATTATCTCTTGACTGA
*
7794 CCAGATTTCCTCATCACGAAGGAACATCGT
1 CCCGATTTCCTCATCACGAAGGAACATCGT
7824 GAGCAGTGTT
Statistics
Matches: 204, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
192 3 0.01
193 201 0.99
ACGTcount: A:0.31, C:0.30, G:0.15, T:0.23
Consensus pattern (193 bp):
CCCGATTTCCTCATCACGAAGGAACATCGTCATAATAAAAAATAACCCGATCTCTTCATCGCAGA
TGAGCAGTGTCGTCTTCAACATCAAACCGACCAGATCTCCTAATCACGAAGGAGCAATGTCACCC
TCAAACAATCAAACTTCCTCATCAGAAAGGAACCGTATTGCCCCCAAATTATCTCTTGACTGA
Found at i:10338 original size:24 final size:24
Alignment explanation
Indices: 10316--10405 Score: 92
Period size: 24 Copynumber: 3.8 Consensus size: 24
10306 GAGATATCAT
* *
10316 AAATCAAAACAGAATTCAGATCAG
1 AAATCAGAACAGAATTCAGATAAG
* * * *
10340 ATATCAGAACAAAATCCATATAAG
1 AAATCAGAACAGAATTCAGATAAG
*
10364 AAATCAGAACAGAATTCAGGTAATG
1 AAATCAGAACAGAATTCAGATAA-G
*
10389 -TATCAGAACAGAATTCA
1 AAATCAGAACAGAATTCA
10406 AGTCGGAAAT
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
24 52 0.98
25 1 0.02
ACGTcount: A:0.51, C:0.16, G:0.13, T:0.20
Consensus pattern (24 bp):
AAATCAGAACAGAATTCAGATAAG
Found at i:10417 original size:24 final size:25
Alignment explanation
Indices: 10316--10419 Score: 67
Period size: 24 Copynumber: 4.3 Consensus size: 25
10306 GAGATATCAT
* *
10316 AAATCAAAACAGAATTC-AGATCA-G
1 AAATCAGAACAGAATTCAAG-TAAGG
* * *
10340 ATATCAGAACAAAATCCATA-TAA-G
1 AAATCAGAACAGAATTCA-AGTAAGG
* *
10364 AAATCAGAACAGAATTCAGGTAATG
1 AAATCAGAACAGAATTCAAGTAAGG
* *
10389 -TATCAGAACAGAATTCAAGT-CGG
1 AAATCAGAACAGAATTCAAGTAAGG
10412 AAATCAGA
1 AAATCAGA
10420 TAAAATATTT
Statistics
Matches: 61, Mismatches: 14, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
23 1 0.02
24 58 0.95
25 1 0.02
26 1 0.02
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.19
Consensus pattern (25 bp):
AAATCAGAACAGAATTCAAGTAAGG
Found at i:22485 original size:23 final size:23
Alignment explanation
Indices: 22459--22503 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
22449 TATATGTTCA
* *
22459 TAAACGTATTCATTTAGTGTTTG
1 TAAACATATACATTTAGTGTTTG
*
22482 TAAACATGTACATTTAGTGTTT
1 TAAACATATACATTTAGTGTTT
22504 ATGAACATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.29, C:0.09, G:0.16, T:0.47
Consensus pattern (23 bp):
TAAACATATACATTTAGTGTTTG
Found at i:22510 original size:23 final size:23
Alignment explanation
Indices: 22469--22513 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
22459 TAAACGTATT
*
22469 CATTTAGTGTTTGTAAACATGTA
1 CATTTAGTGTTTATAAACATGTA
*
22492 CATTTAGTGTTTATGAACATGT
1 CATTTAGTGTTTATAAACATGT
22514 TTGTTCAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (23 bp):
CATTTAGTGTTTATAAACATGTA
Found at i:22823 original size:12 final size:12
Alignment explanation
Indices: 22779--22823 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
22769 AACATAAATG
*
22779 AATGAGTTGATA
1 AATGAGTTCATA
22791 AATGAGCTT-ATA
1 AATGAG-TTCATA
22803 AATGAGTTCATA
1 AATGAGTTCATA
22815 AATGAGTTC
1 AATGAGTTC
22824 GTTCGTTCGT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 2 0.06
12 27 0.87
13 2 0.06
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (12 bp):
AATGAGTTCATA
Found at i:43480 original size:120 final size:114
Alignment explanation
Indices: 43263--43498 Score: 312
Period size: 120 Copynumber: 2.0 Consensus size: 114
43253 AAACCTTTTT
*
43263 TTTGGCTGACACCTGTCTATAAATGATTTTCATCGTTAAAAACACTAATGTGTCATATTTAGCTA
1 TTTGGCTGACACCTGTCTATAAATGATTTTCATCGATAAAAACACTAATGTGTCATATTTAGCTA
* * *
43328 GTCATTTTGCTTGCAATGATATTGAATCATATTTTCTATTGGGTCCTTTG
66 ATCATTTCGCTTGCAATGATATTGAATCATA-TTTCTATTGGGGCCTTTG
* *
43378 TTTGGCTGACACCTAATGTCTATAAATGTTTTTCATTGATAAAAACACTAATGCCT-TCATGATT
1 TTTGGCTGACACC---TGTCTATAAATGATTTTCATCGATAAAAACACTAATG--TGTCAT-ATT
* * * *
43442 TAGTTAATCATTTCGCTTGCAATGATATTGAATTATATTTCTTTTGGGGCTTTTG
60 TAGCTAATCATTTCGCTTGCAATGATATTGAATCATATTTCTATTGGGGCCTTTG
43497 TT
1 TT
43499 ATAATTTGGT
Statistics
Matches: 105, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
115 13 0.12
118 34 0.32
119 21 0.20
120 37 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (114 bp):
TTTGGCTGACACCTGTCTATAAATGATTTTCATCGATAAAAACACTAATGTGTCATATTTAGCTA
ATCATTTCGCTTGCAATGATATTGAATCATATTTCTATTGGGGCCTTTG
Found at i:62797 original size:19 final size:19
Alignment explanation
Indices: 62773--62811 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
62763 TAACTCCGAG
62773 GGCTTGTCTGTCGAGAAGA
1 GGCTTGTCTGTCGAGAAGA
62792 GGCTTGTCTGTCGAGAAGA
1 GGCTTGTCTGTCGAGAAGA
62811 G
1 G
62812 CTCAGTCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.15, G:0.38, T:0.26
Consensus pattern (19 bp):
GGCTTGTCTGTCGAGAAGA
Found at i:68493 original size:18 final size:18
Alignment explanation
Indices: 68462--68508 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
68452 TCTTGTGCAC
68462 AAAAA-AAT-AAATATTT
1 AAAAATAATAAAATATTT
68478 AAAAATAATAAAATATTT
1 AAAAATAATAAAATATTT
* *
68496 AGAAATTATAAAA
1 AAAAATAATAAAA
68509 ATTGAAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 5 0.19
17 3 0.11
18 19 0.70
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
AAAAATAATAAAATATTT
Found at i:70922 original size:15 final size:16
Alignment explanation
Indices: 70889--70923 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
70879 CTAGAGCTGG
*
70889 CAATGCTGACCCAAAC
1 CAATCCTGACCCAAAC
70905 CAATCCTGACCC-AAC
1 CAATCCTGACCCAAAC
70920 CAAT
1 CAAT
70924 TTGAACAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.37, C:0.40, G:0.09, T:0.14
Consensus pattern (16 bp):
CAATCCTGACCCAAAC
Found at i:71976 original size:31 final size:32
Alignment explanation
Indices: 71941--72005 Score: 105
Period size: 34 Copynumber: 2.0 Consensus size: 32
71931 ATAAGTATGC
71941 ACATTAACCATACTC-AAGAAAATATCTAAAT
1 ACATTAACCATACTCAAAGAAAATATCTAAAT
71972 ACATTAACCATACTCTAAAAGAAAATATCTAAAT
1 ACATTAACCATACTC--AAAGAAAATATCTAAAT
72006 CTCAGTTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 15 0.48
34 16 0.52
ACGTcount: A:0.52, C:0.18, G:0.03, T:0.26
Consensus pattern (32 bp):
ACATTAACCATACTCAAAGAAAATATCTAAAT
Found at i:73997 original size:29 final size:29
Alignment explanation
Indices: 73953--74010 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
73943 AAAATAAAAA
* *
73953 ACATAAATAGGGGTTCATTTCTTTTATTT
1 ACATAAATAAGAGTTCATTTCTTTTATTT
73982 ACATAAATAAGAGTTCATTTCTTTTATTT
1 ACATAAATAAGAGTTCATTTCTTTTATTT
74011 CGCCCCGAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (29 bp):
ACATAAATAAGAGTTCATTTCTTTTATTT
Found at i:80947 original size:17 final size:16
Alignment explanation
Indices: 80908--80963 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
80898 CTATAAAAAA
*
80908 ATTAATTAAA-TATAAT
1 ATTAAATAAATTA-AAT
*
80924 ATTAAATAATTTAAAT
1 ATTAAATAAATTAAAT
80940 ACTTAAATAAATT-AAT
1 A-TTAAATAAATTAAAT
*
80956 ATAAAATA
1 ATTAAATA
80964 TACATTAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
15 6 0.18
16 16 0.47
17 12 0.35
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTAAATAAATTAAAT
Found at i:88145 original size:35 final size:34
Alignment explanation
Indices: 88060--88146 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
88050 ATTTGGTATT
*
88060 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
88094 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
88132 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
88147 ACTGAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:88734 original size:18 final size:18
Alignment explanation
Indices: 88711--88745 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
88701 GCGATGGCGG
88711 CATCATATATGGCTGCGA
1 CATCATATATGGCTGCGA
88729 CATCATATATGGCTGCG
1 CATCATATATGGCTGCG
88746 GTGGCTGCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (18 bp):
CATCATATATGGCTGCGA
Found at i:90392 original size:111 final size:111
Alignment explanation
Indices: 90255--90476 Score: 408
Period size: 111 Copynumber: 2.0 Consensus size: 111
90245 ATTACAAAAA
*
90255 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
90320 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
*
90366 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTATTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
90431 AATTAAAACGTTAAAATGTTACCGTATTAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
90477 ATGATTTCCA
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 107 1.00
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:92138 original size:29 final size:30
Alignment explanation
Indices: 92060--92140 Score: 83
Period size: 31 Copynumber: 2.7 Consensus size: 30
92050 TGGAGAATTC
*
92060 AAAAGTTTTAGGATCAATATAGAATGAGGAT
1 AAAAGTTTTAGGATCAATTTAGAAT-AGGAT
* * * * **
92091 AATAGTTTGAGAATGAATTTAGAAT-GTTT
1 AAAAGTTTTAGGATCAATTTAGAATAGGAT
92120 AAAAGTTTTAGGATCAATTTA
1 AAAAGTTTTAGGATCAATTTA
92141 AAATTAAGAA
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
29 19 0.49
31 20 0.51
ACGTcount: A:0.42, C:0.02, G:0.20, T:0.36
Consensus pattern (30 bp):
AAAAGTTTTAGGATCAATTTAGAATAGGAT
Found at i:92438 original size:26 final size:27
Alignment explanation
Indices: 92383--92438 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
92373 TCGTTAAAAA
*
92383 AAATTATTATTTGATTCGTTGCTTGTT
1 AAATTATTATTTGATTCGTTGCTCGTT
* *
92410 AAATTTTTATTTGATTTG-TGCTCGTT
1 AAATTATTATTTGATTCGTTGCTCGTT
92436 AAA
1 AAA
92439 AATATTTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.25, C:0.07, G:0.14, T:0.54
Consensus pattern (27 bp):
AAATTATTATTTGATTCGTTGCTCGTT
Found at i:92915 original size:12 final size:12
Alignment explanation
Indices: 92893--92925 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
92883 CGTTAAGATC
92893 TCAAG-TCGAAT
1 TCAAGTTCGAAT
92904 TCAAGTTCGAAT
1 TCAAGTTCGAAT
*
92916 TCGAGTTCGA
1 TCAAGTTCGA
92926 GTTACTCACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (12 bp):
TCAAGTTCGAAT
Found at i:95432 original size:45 final size:42
Alignment explanation
Indices: 95328--95420 Score: 177
Period size: 42 Copynumber: 2.2 Consensus size: 42
95318 CTGAAGGCGT
*
95328 TGATGGTGTCGGTGTTGGGTGGTAGCCACCACCGCTTCCATG
1 TGATGGTGTCGGAGTTGGGTGGTAGCCACCACCGCTTCCATG
95370 TGATGGTGTCGGAGTTGGGTGGTAGCCACCACCGCTTCCATG
1 TGATGGTGTCGGAGTTGGGTGGTAGCCACCACCGCTTCCATG
95412 TGATGGTGT
1 TGATGGTGT
95421 TTCATGAGTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.13, C:0.22, G:0.37, T:0.29
Consensus pattern (42 bp):
TGATGGTGTCGGAGTTGGGTGGTAGCCACCACCGCTTCCATG
Found at i:109378 original size:36 final size:36
Alignment explanation
Indices: 109326--109438 Score: 115
Period size: 36 Copynumber: 3.1 Consensus size: 36
109316 CTTGCACCAA
109326 TTTCATCTCAGA-CTGCAACAAGGATGTAGCCTTCAG
1 TTTCATCTCA-ATCTGCAACAAGGATGTAGCCTTCAG
***
109362 TTTCATCTCAATCTGCAATTGGGATGTAGCC-TCTAG
1 TTTCATCTCAATCTGCAACAAGGATGTAGCCTTC-AG
* * * *
109398 TTTCATCTC-ATAATGCAGCATGGATGCAGCCTTCAG
1 TTTCATCTCAAT-CTGCAACAAGGATGTAGCCTTCAG
109434 TTTCA
1 TTTCA
109439 GCTCTACCTA
Statistics
Matches: 64, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
35 5 0.08
36 57 0.89
37 2 0.03
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.33
Consensus pattern (36 bp):
TTTCATCTCAATCTGCAACAAGGATGTAGCCTTCAG
Found at i:109517 original size:57 final size:57
Alignment explanation
Indices: 109456--109569 Score: 138
Period size: 57 Copynumber: 2.0 Consensus size: 57
109446 CTACACTCAC
* * *
109456 TTTATCTCAAACTGCAACACGGATGCACCCACCATCTTCATCTTAGCCTGCACCAAT
1 TTTATCTCAAACTGCAACACAGATGCAACCACCATCTTCATCTTAGCATGCACCAAT
* * * * * * *
109513 TTTATCTCAGATTGTAACATAGATGCAATCTCTATCTTCATCTTAGCATGCACCAAT
1 TTTATCTCAAACTGCAACACAGATGCAACCACCATCTTCATCTTAGCATGCACCAAT
109570 GTTTCCATCT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.29, C:0.29, G:0.11, T:0.32
Consensus pattern (57 bp):
TTTATCTCAAACTGCAACACAGATGCAACCACCATCTTCATCTTAGCATGCACCAAT
Found at i:116391 original size:5 final size:5
Alignment explanation
Indices: 116364--116456 Score: 82
Period size: 5 Copynumber: 17.6 Consensus size: 5
116354 TATAATCTTA
* * *
116364 ATTTT ATTGTT ATTTTT ACTTT ATTTT ATCTC ATTTTT ATTTT ATTTT
1 ATTTT ATT-TT A-TTTT ATTTT ATTTT ATTTT A-TTTT ATTTT ATTTT
116412 ATTTT ATTTT ATTTT ATCATTT ATCATTT A--TT ATTTT ATTTT ATT
1 ATTTT ATTTT ATTTT AT--TTT AT--TTT ATTTT ATTTT ATTTT ATT
116457 AATTGTTATT
Statistics
Matches: 75, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
3 3 0.04
5 50 0.67
6 9 0.12
7 13 0.17
ACGTcount: A:0.22, C:0.05, G:0.01, T:0.72
Consensus pattern (5 bp):
ATTTT
Found at i:116402 original size:16 final size:15
Alignment explanation
Indices: 116383--116423 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
116373 TTATTTTTAC
116383 TTTATTTTATCTCATT
1 TTTATTTTATCTCA-T
* *
116399 TTTATTTTATTTTAT
1 TTTATTTTATCTCAT
116414 TTTATTTTAT
1 TTTATTTTAT
116424 TTTATCATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTATTTTATCTCAT
Found at i:116435 original size:32 final size:31
Alignment explanation
Indices: 116366--116456 Score: 87
Period size: 32 Copynumber: 2.8 Consensus size: 31
116356 TAATCTTAAT
* * *
116366 TTTATTGTTATTTTTACTTTATTTTATCTCATT
1 TTTATT-TTA-TTTTATTTTATTTTATTTCATA
*
116399 TTTATTTTATTTTATTTTATTTTATTTTATCA
1 TTTATTTTATTTTATTTTATTTTATTTCAT-A
116431 TTTATCATTTA--TTATTTTATTTTATT
1 TTTAT--TTTATTTTATTTTATTTTATT
116457 AATTGTTATT
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
31 18 0.35
32 23 0.45
33 6 0.12
34 4 0.08
ACGTcount: A:0.21, C:0.05, G:0.01, T:0.73
Consensus pattern (31 bp):
TTTATTTTATTTTATTTTATTTTATTTCATA
Found at i:116582 original size:2 final size:2
Alignment explanation
Indices: 116575--116612 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
116565 GCCGATTGTA
116575 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
116613 ATTATAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:118981 original size:19 final size:18
Alignment explanation
Indices: 118940--118983 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
118930 AAAATAAAAA
**
118940 CATCGATCATAATTTGTG
1 CATCGATCATAATTAATG
*
118958 TATCGATGCATAATTAATG
1 CATCGAT-CATAATTAATG
118977 CATCGAT
1 CATCGAT
118984 ACACATATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (18 bp):
CATCGATCATAATTAATG
Found at i:123140 original size:185 final size:185
Alignment explanation
Indices: 122822--123169 Score: 626
Period size: 185 Copynumber: 1.9 Consensus size: 185
122812 ATTAAATTTT
* *
122822 AAATATTATATATATTATATATAACATATGGGCTCAATCCAAACAATTTAAAACCCAATTAATAA
1 AAATATTATATATATTATATATAACATATGGACTCAACCCAAACAATTTAAAACCCAATTAATAA
*
122887 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAACATTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
122952 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTATTTTTTTAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTATTTTTTTAATTAAA
*
123007 AAATATTATATATATTATATATAACATATGGACT-AAGCCCAAACCATTTAAAACCCAATTAATA
1 AAATATTATATATATTATATATAACATATGGACTCAA-CCCAAACAATTTAAAACCCAATTAATA
* *
123071 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATCTAAATTT
65 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATT
123136 TTTATTTTATAATTATATATTATTTAAATTAATT
130 TTTATTTTATAATTATATATTATTTAAATTAATT
123170 ATTAGCTTTT
Statistics
Matches: 156, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
184 2 0.01
185 154 0.99
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.41
Consensus pattern (185 bp):
AAATATTATATATATTATATATAACATATGGACTCAACCCAAACAATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTATTTTTTTAATTAAA
Found at i:123327 original size:31 final size:30
Alignment explanation
Indices: 123269--123328 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
123259 CCGAAATTTA
**
123269 TTCGGTTCGGTTAATATTTTAGAAAAAAAG
1 TTCGGTTCGGTTAATATTAAAGAAAAAAAG
*
123299 TTCGGTTCGGTTAATGGTTAAAGAAAAAAA
1 TTCGGTTCGGTTAAT-ATTAAAGAAAAAAA
123329 AAGTTTGGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (30 bp):
TTCGGTTCGGTTAATATTAAAGAAAAAAAG
Found at i:142805 original size:103 final size:103
Alignment explanation
Indices: 142689--142879 Score: 303
Period size: 103 Copynumber: 1.9 Consensus size: 103
142679 CAAATGATAA
* * * *
142689 GTCTGCTCCCTATTTCTTCAGAGAGTATAGGACTTGATCTTCAACAAATATGTCCACTCCCTATT
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAACAAACATGTCCACTCCCTATT
142754 CCTTCAGAGAGTATAGG-ACTCGATCTTCAAGAAAATGT
66 CCTTCAGAGAGTAT-GGAACTCGATCTTCAAGAAAATGT
* *
142792 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAATAAACATGTCCGCTCCCTATT
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAACAAACATGTCCACTCCCTATT
*
142857 GCTTCAGAGAGTATGGAACTCGA
66 CCTTCAGAGAGTATGGAACTCGA
142880 ACATCTTCTT
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
102 2 0.03
103 78 0.98
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (103 bp):
GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAACAAACATGTCCACTCCCTATT
CCTTCAGAGAGTATGGAACTCGATCTTCAAGAAAATGT
Found at i:142826 original size:52 final size:50
Alignment explanation
Indices: 142693--142879 Score: 243
Period size: 51 Copynumber: 3.7 Consensus size: 50
142683 TGATAAGTCT
* * *
142693 GCTCCCTATTTCTTCAGAGAGTATAGGACTTGATCTTCAACAAATATGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAAAAAAT-TGTCC
* *
142744 ACTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAAGAAAATGTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAA-AAAAT-TGTCC
*
142796 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAATAAACA-TGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAA-AAA-ATTGTCC
*
142847 GCTCCCTATTGCTTCAGAGAGTAT-GGAACTCGA
1 GCTCCCTATTCCTTCAGAGAGTATAGG-ACTCGA
142880 ACATCTTCTT
Statistics
Matches: 121, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
50 1 0.01
51 70 0.58
52 49 0.40
53 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (50 bp):
GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAAAAAATTGTCC
Found at i:142923 original size:54 final size:54
Alignment explanation
Indices: 142865--143053 Score: 342
Period size: 54 Copynumber: 3.5 Consensus size: 54
142855 TTGCTTCAGA
142865 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
*
142919 GAGTATGGAACTCGAACATTTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
* *
142973 GAGTATGGAACTCGAACATCTTCTTCTTATGGGTTCACTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
*
143027 GAGTATGGAACTTGAACATCTTCTTCT
1 GAGTATGGAACTCGAACATCTTCTTCT
143054 GCTTTACTAC
Statistics
Matches: 130, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 130 1.00
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.37
Consensus pattern (54 bp):
GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
Found at i:143478 original size:37 final size:37
Alignment explanation
Indices: 143427--143549 Score: 153
Period size: 36 Copynumber: 3.4 Consensus size: 37
143417 TTGCTCCAAC
* * *
143427 ACTCTTCCGAGAAGGCTTAAAAAGGATATGCTTCACT
1 ACTCTTCGGTGAAGGCTTAAAAAGGATTTGCTTCACT
*
143464 ACTCTTCGGTGAAGGCTTAAGATA-G-TTTGCTTCACT
1 ACTCTTCGGTGAAGGCTTAA-AAAGGATTTGCTTCACT
* *
143500 ACTCTT-GGTGAAGGCTCAAAATGGATTTGCTTCACT
1 ACTCTTCGGTGAAGGCTTAAAAAGGATTTGCTTCACT
*
143536 ACTCTTTGGTGAAG
1 ACTCTTCGGTGAAG
143550 ACTTGGCTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
34 1 0.01
35 13 0.17
36 33 0.44
37 26 0.35
38 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.33
Consensus pattern (37 bp):
ACTCTTCGGTGAAGGCTTAAAAAGGATTTGCTTCACT
Done.