Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005245.1 Hibiscus syriacus cultivar Beakdansim tig00011868_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: 93818
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:13229 original size:22 final size:22
Alignment explanation
Indices: 13189--13230 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
13179 AATCAATGAT
*
13189 ATAATTTACCTTTTTATTTTAA
1 ATAATTTACCTTTTAATTTTAA
13211 ATAATTTA-CTTTTAAATTTT
1 ATAATTTACCTTTT-AATTTT
13231 TAAACTAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (22 bp):
ATAATTTACCTTTTAATTTTAA
Found at i:24582 original size:15 final size:15
Alignment explanation
Indices: 24562--24599 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
24552 GTTTGCTTCA
24562 GAATGATTAAGCGAT
1 GAATGATTAAGCGAT
* *
24577 GAATGATTAATCGCT
1 GAATGATTAAGCGAT
24592 GAATGATT
1 GAATGATT
24600 TAAATGTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.32
Consensus pattern (15 bp):
GAATGATTAAGCGAT
Found at i:28450 original size:16 final size:16
Alignment explanation
Indices: 28429--28489 Score: 104
Period size: 16 Copynumber: 3.8 Consensus size: 16
28419 TAATAAATAA
28429 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
28445 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
28461 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
*
28477 AAGAACATAAACG
1 ACGAACATAAACG
28490 TTGGAGACCC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.57, C:0.21, G:0.13, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:28753 original size:11 final size:11
Alignment explanation
Indices: 28716--28767 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
28706 TCGAGACTCG
*
28716 AGCTCGATTGA
1 AGCTCGATTCA
* *
28727 AGCTTGATTCTG
1 AGCTCGATTC-A
*
28739 AGCTCGATTCT
1 AGCTCGATTCA
28750 AGCTCGATTCA
1 AGCTCGATTCA
28761 AGCTCGA
1 AGCTCGA
28768 CATTGCCCTA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
11 25 0.74
12 9 0.26
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:28753 original size:23 final size:22
Alignment explanation
Indices: 28713--28767 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 22
28703 AACTCGAGAC
* *
28713 TCGAGCTCGATTGAAGCTTGAT
1 TCGAGCTCGATTCAAGCTCGAT
*
28735 TCTGAGCTCGATTCTAGCTCGAT
1 TC-GAGCTCGATTCAAGCTCGAT
*
28758 TCAAGCTCGA
1 TCGAGCTCGA
28768 CATTGCCCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 9 0.32
23 19 0.68
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.31
Consensus pattern (22 bp):
TCGAGCTCGATTCAAGCTCGAT
Found at i:29469 original size:14 final size:14
Alignment explanation
Indices: 29452--29507 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
29442 ACTGAACATA
*
29452 AACGAACATAACCG
1 AACGAACATAATCG
29466 AACGAACAT-A---
1 AACGAACATAATCG
29476 AACGAACATAATCG
1 AACGAACATAATCG
*
29490 AGCGAACATAATCG
1 AACGAACATAATCG
29504 AACG
1 AACG
29508 TTCACGAACG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
10 9 0.25
11 1 0.03
13 1 0.03
14 25 0.69
ACGTcount: A:0.50, C:0.23, G:0.16, T:0.11
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:29472 original size:24 final size:24
Alignment explanation
Indices: 29445--29506 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
29435 ATAAATGACT
29445 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
* *
29469 GAACATAAACGAACATAATCGAGC
1 GAACATAAACGAACATAACCGAAC
*
29493 GAACATAATCGAAC
1 GAACATAAACGAAC
29507 GTTCACGAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.52, C:0.23, G:0.15, T:0.11
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:32889 original size:291 final size:286
Alignment explanation
Indices: 31790--33062 Score: 1295
Period size: 291 Copynumber: 4.5 Consensus size: 286
31780 TTGCTGTTAA
* * * * *
31790 CGGTGATTGTGATCTTCTTGG-CTTCAGTGTGGGTTGTTCGCTTTCTTTAACATGATCGTCATGT
1 CGGTGATGGTGATCTTCTTGGTCTT-AGTGTGGGTTGTTCGCTTTCTTTATCACGATCATTATGT
* * * * * *
31854 CCCTTAACTTGCTCGGAATTCTCCATTTCCGACTGC--TTCATCGTCACCAACGCGGTCTTTCT-
65 TCCTTATCTTGCTCAGAATCCTCCATTTCCGAGTGCTTTTCACCGTCACCAACGCGGTCTTTCTC
* * * * * * * *
31916 TC-CCAACGGTATCGGTGACGGTGATCTTCTTGTTCTTCGTATGGGTTGTTCACTTTCTTTATCT
130 TCACCAATGGTATCGGTGATGGTGATCTTCTCGGTCTTAGTGTGGGTTGTTCGCTTTCTTTATCA
* ** *
31980 CGATCATTATGTTCCTTATCTTGCTCAGAATCCTCTATTTCGGAGTGTTGCTTCATCGTCACCAA
195 CGATCATTATGTTCCTTATCTTGCTCAGAATCCTCCATTTCGGAGTACTGCTTCACCGTCACCAA
* * *
32045 CGCGGT-TTGT-TC--CCCCATTGGTAT
260 TGCGGTCTT-TCTCATCACCATCGGTAT
* * * * *
32069 CGGTGATGGTGATCTTCTTGTTCTTCGTATGGGTTGTTCACTTTCTTTATCTCGATCATTATGTT
1 CGGTGATGGTGATCTTCTTGGTCTTAGTGTGGGTTGTTCGCTTTCTTTATCACGATCATTATGTT
* * **
32134 CCTTATCTTGCTCAGAATCCTCTATTTCGGAGTG-TTGCTTCGTCGTCACCAACGCGGT-TTT-T
66 CCTTATCTTGCTCAGAATCCTCCATTTCCGAGTGCTT--TTCACCGTCACCAACGCGGTCTTTCT
* * * * *
32196 CCCCCCATTGGTATCGGTGATGGTGATCTTTTTGGTCTTAGTGTAGGGTT-TTCGCTTTCTTTAT
129 CTCACCAATGGTATCGGTGATGGTGATCTTCTCGGTCTTAGTGT-GGGTTGTTCGCTTTCTTTAT
* * ** * ** **
32260 CTCGATCATTATGTTCCTTATCTTGCTCAGAATCCTCCATTTCGGGGTGTTGTTTCGTCGTCGTC
193 CACGATCATTATGTTCCTTATCTTGCTCAGAATCCTCCATTTCGGAGTACTGCTTCACCGTCACC
* *
32325 AATGCGGTCTTTCTCATCACCATTGGCAT
258 AATGCGGTCTTTCTCATCACCATCGGTAT
* * * * * *
32354 CGGTGATGGTGATCTTCTCGGTGTTAATGTGGGTTGTTCGCTGTCTTTATCCCGATCTTTATGTT
1 CGGTGATGGTGATCTTCTTGGTCTTAGTGTGGGTTGTTCGCTTTCTTTATCACGATCATTATGTT
* * * * * * **
32419 TCTCATCTTGCTCAGAATCCTCCATTTCGGAATGCTGCTTCACCGTCACCACCGCCATCTTTCTC
66 CCTTATCTTGCTCAGAATCCTCCATTTCCGAGTGCT-TTTCACCGTCACCAACGCGGTCTTTCTC
* * *
32484 ATCA-CTATCGGTATCGGTGATGGTGATCTTCTCGGTCCTAGTGTGAGTTGTTCGCTTTCTTTAT
130 -TCACCAAT-GGTATCGGTGATGGTGATCTTCTCGGTCTTAGTGTGGGTTGTTCGCTTTCTTTAT
* ** * *
32548 CAGGATCATTATGTTCCTTATCTTGCTCAGAA-CTCTCCAAGTCCGAGTACTGCTTCACCGTAAC
193 CACGATCATTATGTTCCTTATCTTGCTCAGAATC-CTCCATTTCGGAGTACTGCTTCACCGTCAC
* **
32612 CACTGCATTCTTTCTCATCACCATCGGTAT
257 CAATGCGGTCTTTCTCATCACCATCGGTAT
* * * **
32642 CGGTGACGTTGATCTTCTTGGTCCTAGTGTGGGTTGTTCGCTTTCTTTATCGGGATCATTATGTT
1 CGGTGATGGTGATCTTCTTGGTCTTAGTGTGGGTTGTTCGCTTTCTTTATCACGATCATTATGTT
* * * * * * *
32707 CTTTATCTTGCTGATCAGAATTCTCCATGTCCGAGTACTTTTCCACCGTCATCAATGCGGTTTTT
66 CCTTATCTTGC---TCAGAATCCTCCATTTCCGAGTGCTTTT-CACCGTCACCAACGCGGTCTTT
*
32772 CTCATCACCAATGGAATCGGTGATGGTGATCTTCTCGGTCTTAGTGTGGGTTGTTCGCTCTTCTT
127 CTC-TCACCAATGGTATCGGTGATGGTGATCTTCTCGGTCTTAGTGTGGGTTGTTCGCT-TTCTT
* * * *
32837 T-TCACGATCATTATGTTCCTTATCATGCTCGGAATCCTCCGTTTCGGAGTACTGCTTCACAGTC
190 TATCACGATCATTATGTTCCTTATCTTGCTCAGAATCCTCCATTTCGGAGTACTGCTTCACCGTC
* *
32901 ATCAATGCGGTCTTTCTCATCACCATCGGAAT
255 ACCAATGCGGTCTTTCTCATCACCATCGGTAT
* * * *
32933 AGGTGATGGTGATCTT-TTCGGTTTTCGTGTGGG-TGTTTCGCTTTCTTTTTCACGATCATTATG
1 CGGTGATGGTGATCTTCTT-GGTCTTAGTGTGGGTTG-TTCGCTTTCTTTATCACGATCATTATG
* * * * * * * *
32996 TTCCTTATCCTGCTCAGAATCCTCCATCTCGGAGTGCTGCTTCATCGTCATCAACGCGCTCCTTC
64 TTCCTTATCTTGCTCAGAATCCTCCATTTCCGAGTGCT-TTTCACCGTCACCAACGCGGTCTTTC
33061 TC
128 TC
33063 GCCGGCGATC
Statistics
Matches: 817, Mismatches: 147, Indels: 51
0.80 0.14 0.05
Matches are distributed among these distances:
279 78 0.10
280 4 0.00
281 4 0.00
282 132 0.16
283 9 0.01
285 110 0.13
286 4 0.00
287 9 0.01
288 224 0.27
289 2 0.00
290 6 0.01
291 225 0.28
292 10 0.01
ACGTcount: A:0.15, C:0.25, G:0.20, T:0.40
Consensus pattern (286 bp):
CGGTGATGGTGATCTTCTTGGTCTTAGTGTGGGTTGTTCGCTTTCTTTATCACGATCATTATGTT
CCTTATCTTGCTCAGAATCCTCCATTTCCGAGTGCTTTTCACCGTCACCAACGCGGTCTTTCTCT
CACCAATGGTATCGGTGATGGTGATCTTCTCGGTCTTAGTGTGGGTTGTTCGCTTTCTTTATCAC
GATCATTATGTTCCTTATCTTGCTCAGAATCCTCCATTTCGGAGTACTGCTTCACCGTCACCAAT
GCGGTCTTTCTCATCACCATCGGTAT
Found at i:33038 original size:435 final size:426
Alignment explanation
Indices: 31798--33053 Score: 1369
Period size: 435 Copynumber: 2.9 Consensus size: 426
31788 AACGGTGATT
* * * * * *
31798 GTGATCTTCTTGG-CTTCAGTGTGGGTTGTTCGCTTTCTTTAACATGATCGTCATGTCCCTTAAC
1 GTGATCTTCTTGGTCTT-AGTGTGGGTTGTTCGCTTTCTTTATCACGATCATTATGTTCCTTATC
* * * *
31862 TTGCTCGGAATTCTCCATTTCCGA--CTGCTTCATCGTCACCAACGCGGTCTTTCT--TC-CCAA
65 TTGCTCAGAATTCTCCATTTCCGAGTCT-TTTCATCGTCATCAATGCGGTCTTTCTCATCACCAA
* * * * * * * * *
31922 CGGTATCGGTGACGGTGATCTTCTTGTTCTTCGTATGGGTTGTTCACTTTCTTTATCTCGATCAT
129 TGGAATCGGTGATGGTGATCTTCTCGGTCTTAGTGTGGGTTGTTCGCTTTCTTTATCACGATCAT
* *
31987 TATGTTCCTTATCTTGCTCAGAATCCTCTATTTCGGAGTGTTGCTTCATCGTCACCAACGCGGT-
194 TATGTTCCTTATCTTGCTCAGAATCCTCCATTTCGGAGTGCTGCTTCA-CGTCACCAACGCGGTC
* * * *
32051 TTGT-TC--CCCCATTGGTATCGGTGATGGTGATCTTCTT--GTTCTTCGTATGGGTTGTTCACT
258 TT-TCTCATCACCATCGGTATCGGTGATGGTGATCTT-TTCGGTT-TTCGTGTGGGTTGTTCGCT
* * * * *
32111 TTCTTTATCTCGATCATTATGTTCCTTATCTTGCTCAGAATCCTCTATTTCGGAGTGTTGCTTCG
320 TTCTTTATCACGATCATTATGTTCCTTATCTTGCTCAGAATCCTCCATCTCGGAGTGCTGCTTCA
* * * * * *
32176 TCGTCACCAACGCGGTTTTTCCCCCCATTGGTATCGGTGATG
385 CCGTAACCAACGCGATTTTTCCCACCATCGGTATCGGTGACG
* *
32218 GTGATCTTTTTGGTCTTAGTGTAGGGTT-TTCGCTTTCTTTATCTCGATCATTATGTTCCTTATC
1 GTGATCTTCTTGGTCTTAGTGT-GGGTTGTTCGCTTTCTTTATCACGATCATTATGTTCCTTATC
* * * * * *
32282 TTGCTCAGAATCCTCCATTTCGGGGTGTTGTTTCGTCGTCGTCAATGCGGTCTTTCTCATCACCA
65 TTGCTCAGAATTCTCCATTTCCGAGT-CT-TTTCATCGTCATCAATGCGGTCTTTCTCATCACCA
* * * * * * *
32347 TTGGCATCGGTGATGGTGATCTTCTCGGTGTTAATGTGGGTTGTTCGCTGTCTTTATCCCGATCT
128 ATGGAATCGGTGATGGTGATCTTCTCGGTCTTAGTGTGGGTTGTTCGCTTTCTTTATCACGATCA
* * * * **
32412 TTATGTTTCTCATCTTGCTCAGAATCCTCCATTTCGGAATGCTGCTTCACCGTCACCACCGCCAT
193 TTATGTTCCTTATCTTGCTCAGAATCCTCCATTTCGGAGTGCTGCTTCA-CGTCACCAACGCGGT
* * ** * *
32477 CTTTCTCATCACTATCGGTATCGGTGATGGTGATCTTCTCGGTCCTAGTGTGAGTTGTTCGCTTT
257 CTTTCTCATCACCATCGGTATCGGTGATGGTGATCTTTTCGGTTTTCGTGTGGGTTGTTCGCTTT
* ** * *
32542 CTTTATCAGGATCATTATGTTCCTTATCTTGCTCAGAA-CTCTCCAAGTCCGAGTACTGCTTCAC
322 CTTTATCACGATCATTATGTTCCTTATCTTGCTCAGAATC-CTCCATCTCGGAGTGCTGCTTCAC
32606 CGTAACC-ACTGC-ATTCTTTCTCATCACCATCGGTATCGGTGACG
386 CGTAACCAAC-GCGATT-TTTC-C--CACCATCGGTATCGGTGACG
* * ** *
32650 TTGATCTTCTTGGTCCTAGTGTGGGTTGTTCGCTTTCTTTATCGGGATCATTATGTTCTTTATCT
1 GTGATCTTCTTGGTCTTAGTGTGGGTTGTTCGCTTTCTTTATCACGATCATTATGTTCCTTATCT
* * *
32715 TGCTGATCAGAATTCTCCATGTCCGAGTACTTTTCCACCGTCATCAATGCGGTTTTTCTCATCAC
66 TGC---TCAGAATTCTCCATTTCCGAGT-CTTTT-CATCGTCATCAATGCGGTCTTTCTCATCAC
32780 CAATGGAATCGGTGATGGTGATCTTCTCGGTCTTAGTGTGGGTTGTTCGCTCTTCTTT-TCACGA
126 CAATGGAATCGGTGATGGTGATCTTCTCGGTCTTAGTGTGGGTTGTTCGCT-TTCTTTATCACGA
* * * * * *
32844 TCATTATGTTCCTTATCATGCTCGGAATCCTCCGTTTCGGAGTACTGCTTCACAGTCATCAATGC
190 TCATTATGTTCCTTATCTTGCTCAGAATCCTCCATTTCGGAGTGCTGCTTCAC-GTCACCAACGC
* *
32909 GGTCTTTCTCATCACCATCGGAATAGGTGATGGTGATCTTTTCGGTTTTCGTGTGGG-TGTTTCG
254 GGTCTTTCTCATCACCATCGGTATCGGTGATGGTGATCTTTTCGGTTTTCGTGTGGGTTG-TTCG
* *
32973 CTTTCTTTTTCACGATCATTATGTTCCTTATCCTGCTCAGAATCCTCCATCTCGGAGTGCTGCTT
318 CTTTCTTTATCACGATCATTATGTTCCTTATCTTGCTCAGAATCCTCCATCTCGGAGTGCTGCTT
* * *
33038 CATCGTCATCAACGCG
383 CACCGTAACCAACGCG
33054 CTCCTTCTCG
Statistics
Matches: 686, Mismatches: 119, Indels: 46
0.81 0.14 0.05
Matches are distributed among these distances:
420 66 0.10
421 8 0.01
423 24 0.03
425 2 0.00
426 111 0.16
427 4 0.01
428 6 0.01
429 105 0.15
430 3 0.00
431 5 0.01
432 73 0.11
434 6 0.01
435 265 0.39
436 8 0.01
ACGTcount: A:0.15, C:0.25, G:0.20, T:0.40
Consensus pattern (426 bp):
GTGATCTTCTTGGTCTTAGTGTGGGTTGTTCGCTTTCTTTATCACGATCATTATGTTCCTTATCT
TGCTCAGAATTCTCCATTTCCGAGTCTTTTCATCGTCATCAATGCGGTCTTTCTCATCACCAATG
GAATCGGTGATGGTGATCTTCTCGGTCTTAGTGTGGGTTGTTCGCTTTCTTTATCACGATCATTA
TGTTCCTTATCTTGCTCAGAATCCTCCATTTCGGAGTGCTGCTTCACGTCACCAACGCGGTCTTT
CTCATCACCATCGGTATCGGTGATGGTGATCTTTTCGGTTTTCGTGTGGGTTGTTCGCTTTCTTT
ATCACGATCATTATGTTCCTTATCTTGCTCAGAATCCTCCATCTCGGAGTGCTGCTTCACCGTAA
CCAACGCGATTTTTCCCACCATCGGTATCGGTGACG
Found at i:33046 original size:144 final size:144
Alignment explanation
Indices: 31790--33062 Score: 1293
Period size: 144 Copynumber: 8.9 Consensus size: 144
31780 TTGCTGTTAA
* * * * *
31790 CGGTGATTGTGATCTTCTT-GG-CTTCAGTGTGGGTTGTTCGCTTTCTTTAACATGATCGTCATG
1 CGGTGATGGTGATCTT-TTCGGTCTT-AGTGTGGGTTGTTCGCTTTCTTTATCACGATCATTATG
* * * * *
31853 TCCCTTAACTTGCTCGGAATTCTCCATTTCCGA---CTGCTTCATCGTCACCAACGCGGTCTTTC
64 TTCCTTATCTTGCTCAGAATCCTCCATTTCGGAGTGCTGCTTCATCGTCACCAACGCGGTCTTTC
*
31915 T--TC-CCAACGGTAT
129 TCATCACCATCGGTAT
* * * * * *
31928 CGGTGACGGTGATCTTCTT-GTTCTTCGTATGGGTTGTTCACTTTCTTTATCTCGATCATTATGT
1 CGGTGATGGTGATCTT-TTCGGTCTTAGTGTGGGTTGTTCGCTTTCTTTATCACGATCATTATGT
* *
31992 TCCTTATCTTGCTCAGAATCCTCTATTTCGGAGTGTTGCTTCATCGTCACCAACGCGGT-TTGT-
65 TCCTTATCTTGCTCAGAATCCTCCATTTCGGAGTGCTGCTTCATCGTCACCAACGCGGTCTT-TC
* *
32055 TC--CCCCATTGGTAT
129 TCATCACCATCGGTAT
* * * * *
32069 CGGTGATGGTGATCTTCTT-GTTCTTCGTATGGGTTGTTCACTTTCTTTATCTCGATCATTATGT
1 CGGTGATGGTGATCTT-TTCGGTCTTAGTGTGGGTTGTTCGCTTTCTTTATCACGATCATTATGT
* * *
32133 TCCTTATCTTGCTCAGAATCCTCTATTTCGGAGTGTTGCTTCGTCGTCACCAACGCGGT-TTT-T
65 TCCTTATCTTGCTCAGAATCCTCCATTTCGGAGTGCTGCTTCATCGTCACCAACGCGGTCTTTCT
* * *
32196 C-CCCCCATTGGTAT
130 CATCACCATCGGTAT
* *
32210 CGGTGATGGTGATCTTTTTGGTCTTAGTGTAGGGTT-TTCGCTTTCTTTATCTCGATCATTATGT
1 CGGTGATGGTGATCTTTTCGGTCTTAGTGT-GGGTTGTTCGCTTTCTTTATCACGATCATTATGT
* * * * ** *
32274 TCCTTATCTTGCTCAGAATCCTCCATTTCGGGGTGTTGTTTCGTCGTCGTCAATGCGGTCTTTCT
65 TCCTTATCTTGCTCAGAATCCTCCATTTCGGAGTGCTGCTTCATCGTCACCAACGCGGTCTTTCT
* *
32339 CATCACCATTGGCAT
130 CATCACCATCGGTAT
* * * * * *
32354 CGGTGATGGTGATCTTCTCGGTGTTAATGTGGGTTGTTCGCTGTCTTTATCCCGATCTTTATGTT
1 CGGTGATGGTGATCTTTTCGGTCTTAGTGTGGGTTGTTCGCTTTCTTTATCACGATCATTATGTT
* * * * * **
32419 TCTCATCTTGCTCAGAATCCTCCATTTCGGAATGCTGCTTCACCGTCACCACCGCCATCTTTCTC
66 CCTTATCTTGCTCAGAATCCTCCATTTCGGAGTGCTGCTTCATCGTCACCAACGCGGTCTTTCTC
*
32484 ATCACTATCGGTAT
131 ATCACCATCGGTAT
* * * *
32498 CGGTGATGGTGATCTTCTCGGTCCTAGTGTGAGTTGTTCGCTTTCTTTATCAGGATCATTATGTT
1 CGGTGATGGTGATCTTTTCGGTCTTAGTGTGGGTTGTTCGCTTTCTTTATCACGATCATTATGTT
** * * * * **
32563 CCTTATCTTGCTCAGAA-CTCTCCAAGTCCGAGTACTGCTTCACCGTAACC-ACTGCATTCTTTC
66 CCTTATCTTGCTCAGAATC-CTCCATTTCGGAGTGCTGCTTCATCGTCACCAAC-GCGGTCTTTC
32626 TCATCACCATCGGTAT
129 TCATCACCATCGGTAT
* * * **
32642 CGGTGACGTTGATCTTCTT-GGTCCTAGTGTGGGTTGTTCGCTTTCTTTATCGGGATCATTATGT
1 CGGTGATGGTGATCTT-TTCGGTCTTAGTGTGGGTTGTTCGCTTTCTTTATCACGATCATTATGT
* * * * * * * * * *
32706 TCTTTATCTTGCTGATCAGAATTCTCCATGTCCGAGTACT-TTTCCACCGTCATCAATGCGGTTT
65 TCCTTATCTTGC---TCAGAATCCTCCATTTCGGAGTGCTGCTT-CATCGTCACCAACGCGGTCT
*
32770 TTCTCATCACCAAT-GGAAT
126 TTCTCATCACC-ATCGGTAT
*
32789 CGGTGATGGTGATCTTCTCGGTCTTAGTGTGGGTTGTTCGCTCTTCTTT-TCACGATCATTATGT
1 CGGTGATGGTGATCTTTTCGGTCTTAGTGTGGGTTGTTCGCT-TTCTTTATCACGATCATTATGT
* * * * * *
32853 TCCTTATCATGCTCGGAATCCTCCGTTTCGGAGTACTGCTTCA-CAGTCATCAATGCGGTCTTTC
65 TCCTTATCTTGCTCAGAATCCTCCATTTCGGAGTGCTGCTTCATC-GTCACCAACGCGGTCTTTC
*
32917 TCATCACCATCGGAAT
129 TCATCACCATCGGTAT
* * * *
32933 AGGTGATGGTGATCTTTTCGGTTTTCGTGTGGG-TGTTTCGCTTTCTTTTTCACGATCATTATGT
1 CGGTGATGGTGATCTTTTCGGTCTTAGTGTGGGTTG-TTCGCTTTCTTTATCACGATCATTATGT
* * * * *
32997 TCCTTATCCTGCTCAGAATCCTCCATCTCGGAGTGCTGCTTCATCGTCATCAACGCGCTCCTTCT
65 TCCTTATCTTGCTCAGAATCCTCCATTTCGGAGTGCTGCTTCATCGTCACCAACGCGGTCTTTCT
33062 C
130 C
33063 GCCGGCGATC
Statistics
Matches: 981, Mismatches: 122, Indels: 58
0.84 0.11 0.05
Matches are distributed among these distances:
138 75 0.08
139 3 0.00
140 9 0.01
141 271 0.28
142 8 0.01
143 20 0.02
144 471 0.48
145 4 0.00
146 3 0.00
147 108 0.11
148 9 0.01
ACGTcount: A:0.15, C:0.25, G:0.20, T:0.40
Consensus pattern (144 bp):
CGGTGATGGTGATCTTTTCGGTCTTAGTGTGGGTTGTTCGCTTTCTTTATCACGATCATTATGTT
CCTTATCTTGCTCAGAATCCTCCATTTCGGAGTGCTGCTTCATCGTCACCAACGCGGTCTTTCTC
ATCACCATCGGTAT
Found at i:34564 original size:20 final size:20
Alignment explanation
Indices: 34541--34588 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
34531 AGTGAATATT
* *
34541 ATTATTTAAAAACATTTTAA
1 ATTATTTAAAAAAATTTAAA
*
34561 ATTATAATAAAAAAATTTAAA
1 ATTAT-TTAAAAAAATTTAAA
34582 ATT-TTTA
1 ATTATTTA
34589 GAGATAACGA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.09
20 6 0.26
21 15 0.65
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTATTTAAAAAAATTTAAA
Found at i:46086 original size:35 final size:36
Alignment explanation
Indices: 45999--46120 Score: 176
Period size: 35 Copynumber: 3.4 Consensus size: 36
45989 TTATCCCATT
* *
45999 ATCATTTTTC-AACAAACATCTACCAAACTTTAAAA
1 ATCATTTTTCAAAGAAACATTTACCAAACTTTAAAA
*
46034 AACTATTTTTCAAAGAAACATTTACCAAACTTTAAAA
1 ATC-ATTTTTCAAAGAAACATTTACCAAACTTTAAAA
46071 ATCA-TTTTCAAAGAAACATTTACCAAACTTTAAAA
1 ATCATTTTTCAAAGAAACATTTACCAAACTTTAAAA
*
46106 ACCATTTTTTCAAAG
1 ATCA-TTTTTCAAAG
46121 TTGGTTACCA
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
35 36 0.46
36 8 0.10
37 34 0.44
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (36 bp):
ATCATTTTTCAAAGAAACATTTACCAAACTTTAAAA
Found at i:50152 original size:16 final size:16
Alignment explanation
Indices: 50128--50159 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
50118 TATCGCCGAC
*
50128 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
50144 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
50160 TGTGAATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:55792 original size:60 final size:60
Alignment explanation
Indices: 55693--55809 Score: 134
Period size: 60 Copynumber: 1.9 Consensus size: 60
55683 TTTGTCCATG
* * *
55693 AACTATGACCTTACTTTTAAATTGAGCCCTAAATGTTTG-AC-TATTCAAATTCCATCCTGA
1 AACTATGACCTTAATTATAAATTGAGCCCCAAATGTTTGAACAT-TTCAAATT-CATCCTGA
*
55753 AACTATGA-CTCTAATTATAAATT-AGTCCCCAAATTTTTGAACATTTCAAATTCATCC
1 AACTATGACCT-TAATTATAAATTGAG-CCCCAAATGTTTGAACATTTCAAATTCATCC
55810 CTAAAATATG
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
59 4 0.08
60 34 0.69
61 10 0.20
62 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.37
Consensus pattern (60 bp):
AACTATGACCTTAATTATAAATTGAGCCCCAAATGTTTGAACATTTCAAATTCATCCTGA
Found at i:56559 original size:2 final size:2
Alignment explanation
Indices: 56552--56608 Score: 96
Period size: 2 Copynumber: 28.0 Consensus size: 2
56542 CTTTTAAAAT
56552 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
56594 TA TCA TA AA TA TA TA
1 TA T-A TA TA TA TA TA
56609 CAAGTATATG
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 50 0.96
3 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:58361 original size:16 final size:16
Alignment explanation
Indices: 58340--58371 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
58330 GATATCTTTG
58340 AAAAGATCTTCAGCGA
1 AAAAGATCTTCAGCGA
58356 AAAAGATCTTCAGCGA
1 AAAAGATCTTCAGCGA
58372 GCATGTTAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (16 bp):
AAAAGATCTTCAGCGA
Found at i:60446 original size:38 final size:36
Alignment explanation
Indices: 60370--60446 Score: 84
Period size: 37 Copynumber: 2.1 Consensus size: 36
60360 TTTTTATATT
*
60370 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* * *
60406 TTTAATTTTTTTAAAGAAAA-TGTATAAATATTTTACAA
1 TTTAA-TTTTGTAAA-AAAATTATATAAATATTAT-CAA
60444 TTT
1 TTT
60447 GTAATATTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
36 5 0.15
37 20 0.59
38 9 0.26
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.48
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:60628 original size:20 final size:20
Alignment explanation
Indices: 60592--60629 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
60582 ATCATATTCC
**
60592 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTGCATTCCCA
60612 CTGGTAATCTTGCATTCC
1 CTGGTAATCTTGCATTCC
60630 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.26, G:0.13, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTGCATTCCCA
Found at i:64718 original size:60 final size:60
Alignment explanation
Indices: 64654--64773 Score: 141
Period size: 60 Copynumber: 2.0 Consensus size: 60
64644 AATACACAGG
* * * * * *
64654 TGGTCCCCTTATTATAGAGTATTGATTTATTAAGTCCTTCGACTGTTAAAAGTTACAAAA
1 TGGTCACCTGATTATAGAGTATTGAATTATCAAGTCCTTCAACTATTAAAAGTTACAAAA
* * * * *
64714 TGGTCATCTGATTATAGAGTTTTGAATTGTCGAGTCCTTCAACTATTAAAAGTTATAAAA
1 TGGTCACCTGATTATAGAGTATTGAATTATCAAGTCCTTCAACTATTAAAAGTTACAAAA
64774 CGATCACCGC
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (60 bp):
TGGTCACCTGATTATAGAGTATTGAATTATCAAGTCCTTCAACTATTAAAAGTTACAAAA
Found at i:65819 original size:19 final size:20
Alignment explanation
Indices: 65792--65842 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
65782 AAATAACCAA
* *
65792 CAAAATCGCAACGC-GATTC
1 CAAATTCGCAACACAGATTC
*
65811 CAAATTCGCAACACAGTTTC
1 CAAATTCGCAACACAGATTC
*
65831 CAAATTTGCAAC
1 CAAATTCGCAAC
65843 TCGAACATGG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.37, C:0.29, G:0.12, T:0.22
Consensus pattern (20 bp):
CAAATTCGCAACACAGATTC
Found at i:66716 original size:2 final size:2
Alignment explanation
Indices: 66709--66741 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
66699 TTAATTGAGC
66709 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
66742 GATACTATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:68584 original size:14 final size:14
Alignment explanation
Indices: 68565--68626 Score: 61
Period size: 14 Copynumber: 4.0 Consensus size: 14
68555 TGCTGGGAAT
68565 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
68579 CCGAGGCCATCCAAGAGCA
1 CCGAGGCCATCC----G-A
68598 TCCGAGGCCATCCGA
1 -CCGAGGCCATCCGA
*
68613 CCGAGGGCATCCGA
1 CCGAGGCCATCCGA
68627 GGGCAACCGA
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
14 25 0.61
15 1 0.02
16 1 0.02
18 1 0.02
19 1 0.02
20 12 0.29
ACGTcount: A:0.24, C:0.39, G:0.29, T:0.08
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:68636 original size:24 final size:24
Alignment explanation
Indices: 68595--68641 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
68585 CCATCCAAGA
*
68595 GCATCCGAGGCCATCCGACCGAGG
1 GCATCCGAGGCCAACCGACCGAGG
* *
68619 GCATCCGAGGGCAACCGAGCGAG
1 GCATCCGAGGCCAACCGACCGAG
68642 CTATGCGAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.23, C:0.34, G:0.36, T:0.06
Consensus pattern (24 bp):
GCATCCGAGGCCAACCGACCGAGG
Found at i:68637 original size:34 final size:34
Alignment explanation
Indices: 68565--68637 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
68555 TGCTGGGAAT
*
68565 CCGAGGCCATCCGACCGAGGCCATCCAAGAGCAT
1 CCGAGGCCATCCGACCGAGGCCATCCAAGAGCAA
* * *
68599 CCGAGGCCATCCGACCGAGGGCATCCGAGGGCAA
1 CCGAGGCCATCCGACCGAGGCCATCCAAGAGCAA
68633 CCGAG
1 CCGAG
68638 CGAGCTATGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.25, C:0.37, G:0.32, T:0.07
Consensus pattern (34 bp):
CCGAGGCCATCCGACCGAGGCCATCCAAGAGCAA
Found at i:68763 original size:10 final size:10
Alignment explanation
Indices: 68709--68800 Score: 67
Period size: 10 Copynumber: 8.5 Consensus size: 10
68699 TCTTGTAGGT
68709 TGCCCTCGGA
1 TGCCCTCGGA
* *
68719 TTCCCTCGCA
1 TGCCCTCGGA
*
68729 TAGCTCGCTCGGT
1 T-GC-C-CTCGGA
68742 TGCCCTCGGA
1 TGCCCTCGGA
68752 TGCCCTCGGA
1 TGCCCTCGGA
**
68762 TGCTTTCGGA
1 TGCCCTCGGA
68772 TGGCCTCGGTCGGA
1 T-GCC-C--TCGGA
*
68786 TGGCCTCGGA
1 TGCCCTCGGA
68796 TGCCC
1 TGCCC
68801 AGCGTGTTGG
Statistics
Matches: 63, Mismatches: 12, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
10 42 0.67
11 4 0.06
12 4 0.06
13 7 0.11
14 6 0.10
ACGTcount: A:0.09, C:0.36, G:0.30, T:0.25
Consensus pattern (10 bp):
TGCCCTCGGA
Found at i:68786 original size:14 final size:14
Alignment explanation
Indices: 68767--68794 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
68757 TCGGATGCTT
68767 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
68781 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
68795 ATGCCCAGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.43, T:0.21
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:74850 original size:21 final size:21
Alignment explanation
Indices: 74826--74865 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
74816 TGTTATGGAG
*
74826 TTATGATTTAGGGTTTAAGAC
1 TTATAATTTAGGGTTTAAGAC
74847 TTATAATTTAGGGTTTAAG
1 TTATAATTTAGGGTTTAAG
74866 TTAGAGGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.03, G:0.23, T:0.45
Consensus pattern (21 bp):
TTATAATTTAGGGTTTAAGAC
Found at i:78528 original size:5 final size:5
Alignment explanation
Indices: 78518--78556 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
78508 ACCACGACCA
* * *
78518 CGAGC CGAGC CGAGC CGTGC CGAGC CGTGC CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
78557 ACGGATGGCG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.18, C:0.36, G:0.41, T:0.05
Consensus pattern (5 bp):
CGAGC
Done.