Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001759.1 Hibiscus syriacus cultivar Beakdansim tig00003555_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: 76325
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4498 original size:19 final size:19
Alignment explanation
Indices: 4474--4525 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
4464 AAAAGCCCAA
4474 GTGCATCGATGCATGGTGT
1 GTGCATCGATGCATGGTGT
4493 GTGCATCGATGCATGGTGT
1 GTGCATCGATGCATGGTGT
4512 GTGCATCGATGCAT
1 GTGCATCGATGCAT
4526 AAAATGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.17, C:0.17, G:0.35, T:0.31
Consensus pattern (19 bp):
GTGCATCGATGCATGGTGT
Found at i:4590 original size:84 final size:83
Alignment explanation
Indices: 4430--4590 Score: 252
Period size: 84 Copynumber: 1.9 Consensus size: 83
4420 GCACTAAGCA
* *
4430 TGCATCGATGCATAAAATGCATTCAATGTTTTGTAAAAGCCCAAGTGCATCGATGCATGGTGTGT
1 TGCATCGATGCATAAAATGCATTCAATGTTTTGTAAAAGCCCAAGTGCATCGATGCATGGAGAGT
4495 GCATCGATGCATGGTGTG
66 GCATCGATGCATGGTGTG
* *
4513 TGCATCGATGCATAAAATGCATTCGATGTTTTCATTAAAA-CCCAAGTGCATCGATGCATGGAGA
1 TGCATCGATGCATAAAATGCATTCAATGTTTT--GTAAAAGCCCAAGTGCATCGATGCATGGAGA
*
4577 GTGCATCGGTGCAT
64 GTGCATCGATGCAT
4591 TAATTGCATT
Statistics
Matches: 71, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
83 31 0.44
84 35 0.49
85 5 0.07
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (83 bp):
TGCATCGATGCATAAAATGCATTCAATGTTTTGTAAAAGCCCAAGTGCATCGATGCATGGAGAGT
GCATCGATGCATGGTGTG
Found at i:4604 original size:83 final size:81
Alignment explanation
Indices: 4409--4605 Score: 236
Period size: 83 Copynumber: 2.4 Consensus size: 81
4399 TGGAACACTT
* *
4409 AGTGCATCGGTGCACTAAGCATGCATCGATGCATAAAATGCATTCAATGTTTTGTAAAAGCCCAA
1 AGTGCATCGGTGCATTAA--TTGCATCGATGCATAAAATGCATTCAATGTTTTGTAAAAGCCCAA
*
4474 GTGCATCGATGCATGGTG
64 GTGCATCGATGCATGGAG
* * * * *
4492 TGTGCATCGATGCATGGT-GTGTGCATCGATGCATAAAATGCATTCGATGTTTTCATTAAAA-CC
1 AGTGCATCGGTGCAT--TAAT-TGCATCGATGCATAAAATGCATTCAATGTTTT--GTAAAAGCC
4555 CAAGTGCATCGATGCATGGAG
61 CAAGTGCATCGATGCATGGAG
4576 AGTGCATCGGTGCATTAATTGCATTCGATG
1 AGTGCATCGGTGCATTAATTGCA-TCGATG
4606 TTCAATTTAA
Statistics
Matches: 96, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
82 5 0.05
83 50 0.52
84 35 0.36
85 6 0.06
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (81 bp):
AGTGCATCGGTGCATTAATTGCATCGATGCATAAAATGCATTCAATGTTTTGTAAAAGCCCAAGT
GCATCGATGCATGGAG
Found at i:9140 original size:83 final size:85
Alignment explanation
Indices: 9033--9209 Score: 286
Period size: 88 Copynumber: 2.1 Consensus size: 85
9023 GCACTTCTAT
* *
9033 TTAATGAAAACTCTACGTGCACAATCCACAATA-A-TATGAATCTTTTATAAATCAGTATGATCA
1 TTAAGGAAAACTCTACGTGCACAATCCACAATATATTATGAATCTTTTATAAATCAGTATAATCA
*
9096 GTATGATATAAAATATTGAC
66 GTATGATACAAAATATTGAC
9116 TTAAGGAAAACTCTACGTGCACAATCCACAATATTATGTTATGAATCTTTTATAAATCAGTATAA
1 TTAAGGAAAACTCTACGTGCACAATCCACAATA-TA--TTATGAATCTTTTATAAATCAGTATAA
9181 TCAGTATGATACAAAATATTGAC
63 TCAGTATGATACAAAATATTGAC
9204 TTAAGG
1 TTAAGG
9210 GTCACCTTTG
Statistics
Matches: 86, Mismatches: 3, Indels: 5
0.91 0.03 0.05
Matches are distributed among these distances:
83 32 0.37
85 1 0.01
88 53 0.62
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (85 bp):
TTAAGGAAAACTCTACGTGCACAATCCACAATATATTATGAATCTTTTATAAATCAGTATAATCA
GTATGATACAAAATATTGAC
Found at i:14745 original size:21 final size:22
Alignment explanation
Indices: 14699--14753 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
14689 TAGAACGCTG
*
14699 AAGGAATTCTTCAACACGATGC
1 AAGGATTTCTTCAACACGATGC
14721 -AGGATTTCTTCAACAC-ACT-C
1 AAGGATTTCTTCAACACGA-TGC
14741 AAGGATTTTCTTC
1 AAGGA-TTTCTTC
14754 TGCAGATGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 2 0.07
21 20 0.69
22 7 0.24
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (22 bp):
AAGGATTTCTTCAACACGATGC
Found at i:17338 original size:18 final size:18
Alignment explanation
Indices: 17317--17351 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17307 TTCTTCTCCT
*
17317 TCTTTCTCTCTTTCTCTA
1 TCTTTCTCTCTATCTCTA
*
17335 TCTTTTTCTCTATCTCT
1 TCTTTCTCTCTATCTCT
17352 TTCTCCTCCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.06, C:0.31, G:0.00, T:0.63
Consensus pattern (18 bp):
TCTTTCTCTCTATCTCTA
Found at i:17342 original size:12 final size:12
Alignment explanation
Indices: 17323--17356 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
17313 TCCTTCTTTC
17323 TCTCTTTCTCTA
1 TCTCTTTCTCTA
*
17335 TCTTTTTCTCTA
1 TCTCTTTCTCTA
17347 TCTCTTTCTC
1 TCTCTTTCTC
17357 CTCCCCGCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.32, G:0.00, T:0.62
Consensus pattern (12 bp):
TCTCTTTCTCTA
Found at i:23137 original size:2 final size:2
Alignment explanation
Indices: 23132--23168 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
23122 AAAACATCAT
23132 TA TA 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 TA TA T
23169 GGGAACGGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:26107 original size:24 final size:24
Alignment explanation
Indices: 26079--26126 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
26069 TAATAGTTAC
26079 CTATGTTGATAATCTCTTTTTTGA
1 CTATGTTGATAATCTCTTTTTTGA
26103 CTATGTTGATAATCTCTTTTTTGA
1 CTATGTTGATAATCTCTTTTTTGA
26127 TCTTTTTCTT
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:0.21, C:0.12, G:0.12, T:0.54
Consensus pattern (24 bp):
CTATGTTGATAATCTCTTTTTTGA
Found at i:28080 original size:82 final size:82
Alignment explanation
Indices: 27941--28419 Score: 647
Period size: 82 Copynumber: 5.8 Consensus size: 82
27931 CCTTGTAGAC
* * * * * *
27941 AATCTACACTATTGACGTCCTTTGCTTATCATTGACACTTCACATTAACTCAAATAAACTGAAAT
1 AATCTATACTATTCACGTCCTTTGCTTGTCATTGACATTTCACATCAACTCAGATAAACTGAAAT
* *
28006 ATTTTAGTGGATCAGAG
66 ATTTTAGAGAATCAGAG
* * *
28023 AATCTACACTATTTACGTCATTTGCTTGTCATTGACATTTCACATCAACTCAGATAAACTGAAAT
1 AATCTATACTATTCACGTCCTTTGCTTGTCATTGACATTTCACATCAACTCAGATAAACTGAAAT
*
28088 ATTTTAGAGAATCAGGG
66 ATTTTAGAGAATCAGAG
* * * * *
28105 AATCCATACTATTCACATCATTTGCTTGTCATTGATATTTCACATCAACTCAGATAATCTGAAAT
1 AATCTATACTATTCACGTCCTTTGCTTGTCATTGACATTTCACATCAACTCAGATAAACTGAAAT
* *
28170 AATTTCCATTGA-AATCAAAG
66 -ATTT---TAGAGAATCAGAG
28190 AATCTATACTATTCACGTCCTTTGCTTGTCACTT-ACATTTCACATCAACTCAGATAAACTGAAA
1 AATCTATACTATTCACGTCCTTTGCTTGTCA-TTGACATTTCACATCAACTCAGATAAACTGAAA
*
28254 TATTTTAGAGAATCAGGG
65 TATTTTAGAGAATCAGAG
*
28272 ACTCTATACTATTCACGTCCTTTGCTTGTCATTGACATTTCACATCAACTCAGATAAACTGAAAT
1 AATCTATACTATTCACGTCCTTTGCTTGTCATTGACATTTCACATCAACTCAGATAAACTGAAAT
* *
28337 ATTTTAGAGAACCAGGG
66 ATTTTAGAGAATCAGAG
* * * * *
28354 AATTTATACTATTCACGTCCTTTGCTTATCATTTATATTTCACATCAACTCAGATAAATTGAAAT
1 AATCTATACTATTCACGTCCTTTGCTTGTCATTGACATTTCACATCAACTCAGATAAACTGAAAT
28419 A
66 A
28420 ATTTCCATTG
Statistics
Matches: 356, Mismatches: 34, Indels: 14
0.88 0.08 0.03
Matches are distributed among these distances:
81 5 0.01
82 275 0.77
83 4 0.01
84 4 0.01
85 63 0.18
86 5 0.01
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Consensus pattern (82 bp):
AATCTATACTATTCACGTCCTTTGCTTGTCATTGACATTTCACATCAACTCAGATAAACTGAAAT
ATTTTAGAGAATCAGAG
Found at i:28394 original size:249 final size:249
Alignment explanation
Indices: 27941--28451 Score: 792
Period size: 249 Copynumber: 2.1 Consensus size: 249
27931 CCTTGTAGAC
* *
27941 AATCTACACTATTGACGTCCTTTGCTTATCATTGACACTTCACATTAACTCAAATAAACTGAAAT
1 AATCTACACTATTCACGTCCTTTGCTTATCATTGACACTTCACATCAACTCAAATAAACTGAAAT
* * *
28006 ATTTTAGTGGATCAGAGAATCTACACTATTTACGTCATTTGCTTGTCATTGACATTTCACATCAA
66 ATTTTAGAGAATCAGAGAATCTACACTATTCACGTCATTTGCTTGTCATTGACATTTCACATCAA
* *
28071 CTCAGATAAACTGAAATATTTTAGAGAATCAGGGAATCCATACTATTCACATCATTTGCTTGTCA
131 CTCAGATAAACTGAAATATTTTAGAGAACCAGGGAATCCATACTATTCACATCATTTGCTTATCA
28136 TTGATATTTCACATCAACTCAGAT-AATCTGAAATAATTTCCATTGAAATCAAAG
196 TTGATATTTCACATCAACTCAGATAAAT-TGAAATAATTTCCATTGAAATCAAAG
* * * *
28190 AATCTATACTATTCACGTCCTTTGCTTGTCACTT-ACATTTCACATCAACTCAGATAAACTGAAA
1 AATCTACACTATTCACGTCCTTTGCTTATCA-TTGACACTTCACATCAACTCAAATAAACTGAAA
* * * *
28254 TATTTTAGAGAATCAGGGACTCTATACTATTCACGTCCTTTGCTTGTCATTGACATTTCACATCA
65 TATTTTAGAGAATCAGAGAATCTACACTATTCACGTCATTTGCTTGTCATTGACATTTCACATCA
** * *
28319 ACTCAGATAAACTGAAATATTTTAGAGAACCAGGGAATTTATACTATTCACGTCCTTTGCTTATC
130 ACTCAGATAAACTGAAATATTTTAGAGAACCAGGGAATCCATACTATTCACATCATTTGCTTATC
* *
28384 ATTTATATTTCACATCAACTCAGATAAATTGAAATAATTTCCATTGAAATCAGAG
195 ATTGATATTTCACATCAACTCAGATAAATTGAAATAATTTCCATTGAAATCAAAG
*
28439 AATCTACAGTATT
1 AATCTACACTATT
28452 TATATTCTTT
Statistics
Matches: 237, Mismatches: 23, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
249 232 0.98
250 5 0.02
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Consensus pattern (249 bp):
AATCTACACTATTCACGTCCTTTGCTTATCATTGACACTTCACATCAACTCAAATAAACTGAAAT
ATTTTAGAGAATCAGAGAATCTACACTATTCACGTCATTTGCTTGTCATTGACATTTCACATCAA
CTCAGATAAACTGAAATATTTTAGAGAACCAGGGAATCCATACTATTCACATCATTTGCTTATCA
TTGATATTTCACATCAACTCAGATAAATTGAAATAATTTCCATTGAAATCAAAG
Found at i:28465 original size:167 final size:164
Alignment explanation
Indices: 27941--28419 Score: 638
Period size: 167 Copynumber: 2.9 Consensus size: 164
27931 CCTTGTAGAC
* * * * * * * *
27941 AATCTACACTATTGACGTCCTTTGCTTATCATTGACACTTCACATTAACTCAAATAAACTGAAAT
1 AATCTATACTATTCACATTCTTTGCTTGTCATTGACATTTCACATCAACTCAGATAAACTGAAAT
* * * * * *
28006 ATTTTAGTGGATCAGAGAATCTACACTATTTACGTCATTTGCTTGTCATTGACATTTCACATCAA
66 ATTTTAGAGAATCAGAGAATCTATACTATTCACGTCCTTTGCTTGTCATTTACATTTCACATCAA
28071 CTCAGATAAACTGAAATATTTTAGAGAATCAGGG
131 CTCAGATAAACTGAAATATTTTAGAGAATCAGGG
* * *
28105 AATCCATACTATTCACA-TCATTTGCTTGTCATTGATATTTCACATCAACTCAGATAATCTGAAA
1 AATCTATACTATTCACATTC-TTTGCTTGTCATTGACATTTCACATCAACTCAGATAAACTGAAA
* * *
28169 TAATTTCCATTGA-AATCAAAGAATCTATACTATTCACGTCCTTTGCTTGTCACTTACATTTCAC
65 T-ATTT---TAGAGAATCAGAGAATCTATACTATTCACGTCCTTTGCTTGTCATTTACATTTCAC
28233 ATCAACTCAGATAAACTGAAATATTTTAGAGAATCAGGG
126 ATCAACTCAGATAAACTGAAATATTTTAGAGAATCAGGG
* * *
28272 ACTCTATACTATTCACGTCCTTTGCTTGTCATTGACATTTCACATCAACTCAGATAAACTGAAAT
1 AATCTATACTATTCACATTCTTTGCTTGTCATTGACATTTCACATCAACTCAGATAAACTGAAAT
* * * * *
28337 ATTTTAGAGAACCAGGGAATTTATACTATTCACGTCCTTTGCTTATCATTTATATTTCACATCAA
66 ATTTTAGAGAATCAGAGAATCTATACTATTCACGTCCTTTGCTTGTCATTTACATTTCACATCAA
*
28402 CTCAGATAAATTGAAATA
131 CTCAGATAAACTGAAATA
28420 ATTTCCATTG
Statistics
Matches: 273, Mismatches: 35, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
163 4 0.01
164 118 0.43
165 4 0.01
166 4 0.01
167 140 0.51
168 3 0.01
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Consensus pattern (164 bp):
AATCTATACTATTCACATTCTTTGCTTGTCATTGACATTTCACATCAACTCAGATAAACTGAAAT
ATTTTAGAGAATCAGAGAATCTATACTATTCACGTCCTTTGCTTGTCATTTACATTTCACATCAA
CTCAGATAAACTGAAATATTTTAGAGAATCAGGG
Found at i:38613 original size:20 final size:20
Alignment explanation
Indices: 38588--38626 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
38578 CTCGAGACCG
*
38588 TTGGTCTCCATACTGAAGGA
1 TTGGTCTCCATACCGAAGGA
38608 TTGGTCTCCATACCGAAGG
1 TTGGTCTCCATACCGAAGG
38627 CCTAATATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (20 bp):
TTGGTCTCCATACCGAAGGA
Found at i:51999 original size:39 final size:38
Alignment explanation
Indices: 51945--52058 Score: 155
Period size: 34 Copynumber: 3.1 Consensus size: 38
51935 AAAGTCAAGT
* *
51945 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTGTAAGC
1 CTTCACCGAAGAGTAGTGAAGCAAATCCA-TCTGTAAGC
51984 CTTCACCGAAGAGTAGTGAAGC--A-CCATCT-TAAGC
1 CTTCACCGAAGAGTAGTGAAGCAAATCCATCTGTAAGC
* *
52018 CTTCACGGAAGAGTAGTGAAGCAAATTCATCTGTAAGC
1 CTTCACCGAAGAGTAGTGAAGCAAATCCATCTGTAAGC
52056 CTT
1 CTT
52059 TAGAGCAAGA
Statistics
Matches: 67, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
34 26 0.39
35 2 0.03
36 4 0.06
37 6 0.09
38 8 0.12
39 21 0.31
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (38 bp):
CTTCACCGAAGAGTAGTGAAGCAAATCCATCTGTAAGC
Found at i:52415 original size:215 final size:215
Alignment explanation
Indices: 52044--52471 Score: 777
Period size: 215 Copynumber: 2.0 Consensus size: 215
52034 TGAAGCAAAT
*
52044 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGG
1 TCATCTGTAAGCCTTTAGAGCAACATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGG
*
52109 ATGTTTTTACATGAATTTGAAAATGAAAAAACGATGTTTTGAGAAGATGAAATTTTTGAAAACAA
66 ATGTTTTCACATGAATTTGAAAATGAAAAAACGATGTTTTGAGAAGATGAAATTTTTGAAAACAA
52174 AGAATGCGATTTTCAAAATTTCACAATTTATAAG-CCTGTCAGGCCATCAGTAAGTCTTTCGAGC
131 AGAATGCGATTTTCAAAATTTCACAATTTATAAGCCCT-TCAGGCCATCAGTAAGTCTTTCGAGC
*
52238 ATGATGCTTAAATCCTTCGGG
195 ATGATGATTAAATCCTTCGGG
* *
52259 TCATCTGTAAGCCTTTAGAGCAACATGATAAGTCCTTCGGGCCATCCGTAAAACCTTTGGGTAGG
1 TCATCTGTAAGCCTTTAGAGCAACATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGG
52324 ATGTTTTCACATGAATTTGAAAATGAAAAAACGATGTTTTGAGAAGATGAAATTTTTGAAAACAA
66 ATGTTTTCACATGAATTTGAAAATGAAAAAACGATGTTTTGAGAAGATGAAATTTTTGAAAACAA
* *
52389 AGAATGCGATTTTCAAAATTTCACAATTTATAAGCCCTTCGGGCCATTAGTAAGTCTTTCGAGCA
131 AGAATGCGATTTTCAAAATTTCACAATTTATAAGCCCTTCAGGCCATCAGTAAGTCTTTCGAGCA
52454 TGATGATTAAATCCTTCG
196 TGATGATTAAATCCTTCG
52472 AGTAATTTGC
Statistics
Matches: 205, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
215 202 0.99
216 3 0.01
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.31
Consensus pattern (215 bp):
TCATCTGTAAGCCTTTAGAGCAACATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGG
ATGTTTTCACATGAATTTGAAAATGAAAAAACGATGTTTTGAGAAGATGAAATTTTTGAAAACAA
AGAATGCGATTTTCAAAATTTCACAATTTATAAGCCCTTCAGGCCATCAGTAAGTCTTTCGAGCA
TGATGATTAAATCCTTCGGG
Found at i:52530 original size:13 final size:13
Alignment explanation
Indices: 52512--52536 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52502 TGAAGCAAAT
52512 CCATCAGTAAGTG
1 CCATCAGTAAGTG
52525 CCATCAGTAAGT
1 CCATCAGTAAGT
52537 CTTTCGAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:52849 original size:53 final size:53
Alignment explanation
Indices: 52628--52833 Score: 263
Period size: 53 Copynumber: 3.9 Consensus size: 53
52618 ATCACACCAT
* *
52628 AAGATTGTTCGAGTTCTACTCCATGAAGCAAGAGGGAGCGAACCCATAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * *
52681 AATATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGCGAACTCGTAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * * *
52734 AAGACTGTTCAAGTTCTACTCCCTTAAGCAAGAGGTAGCGAACCCGCT-GGTC-G
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCG-TAGG-CAG
* * **
52787 GAGATTGTTCGAGTTCTACTCCCTGAAGCAATAGGGAGAAAACCCGT
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGT
52834 TTGTTGAAGA
Statistics
Matches: 131, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
52 1 0.01
53 128 0.98
54 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (53 bp):
AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
Found at i:56358 original size:33 final size:33
Alignment explanation
Indices: 56320--56410 Score: 164
Period size: 33 Copynumber: 2.8 Consensus size: 33
56310 TCACTTGTAT
*
56320 CATTCTTGTATGATCTCATAAATCATTGTATAA
1 CATTCTTGTATGATCTCATAGATCATTGTATAA
56353 CATTCTTGTATGATCTCATAGATCATTGTATAA
1 CATTCTTGTATGATCTCATAGATCATTGTATAA
*
56386 CATTCTTATATGATCTCATAGATCA
1 CATTCTTGTATGATCTCATAGATCA
56411 CTTTCCATAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (33 bp):
CATTCTTGTATGATCTCATAGATCATTGTATAA
Found at i:63515 original size:20 final size:20
Alignment explanation
Indices: 63490--63557 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
63480 TTTTCCTGAT
63490 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
*
63510 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATATGTAAA
* *
63530 TCGCAATGCGAATCTGTAAA
1 TCGCAACGCGAATATGTAAA
63550 TCGCAACG
1 TCGCAACG
63558 AGATTCTGAC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:64439 original size:24 final size:24
Alignment explanation
Indices: 64412--64465 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
64402 GTATTCGAAA
64412 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
64436 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
64460 TTTGAT
1 TTTGAT
64466 GATTTTTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:66905 original size:20 final size:20
Alignment explanation
Indices: 66880--66968 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
66870 TAAAGCGGAA
66880 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
66900 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* *
66920 ATCGCAATGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
66940 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
*
66960 ATCGTAACG
1 ATCGCAACG
66969 AGATAATCGC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 58 0.95
21 3 0.05
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:66997 original size:19 final size:19
Alignment explanation
Indices: 66973--67018 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
66963 GTAACGAGAT
66973 AATCGCAATGCAAAATGAA
1 AATCGCAATGCAAAATGAA
*
66992 AATCGCAATGCGAAATGAA
1 AATCGCAATGCAAAATGAA
67011 AATCGCAA
1 AATCGCAA
67019 CGAGTGAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCAAAATGAA
Found at i:67021 original size:52 final size:54
Alignment explanation
Indices: 66940--67045 Score: 146
Period size: 52 Copynumber: 2.0 Consensus size: 54
66930 GGAATTGACT
** *
66940 ATCGCAACGCGGAAATGACTATCGTAACGAGAT-AATCGCAATGC-AAAATGAAA
1 ATCGCAACGCGGAAATGAAAATCGCAACGAG-TGAATCGCAATGCAAAAATGAAA
*
66993 ATCGCAATGC-GAAATGAAAATCGCAACGAGTGAATCGCAATGCAAAAATGAAA
1 ATCGCAACGCGGAAATGAAAATCGCAACGAGTGAATCGCAATGCAAAAATGAAA
67046 TTCAGTCGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
51 1 0.02
52 28 0.60
53 18 0.38
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.16
Consensus pattern (54 bp):
ATCGCAACGCGGAAATGAAAATCGCAACGAGTGAATCGCAATGCAAAAATGAAA
Found at i:67214 original size:14 final size:14
Alignment explanation
Indices: 67195--67231 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
67185 CATCAATTAA
67195 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
67209 ACAAATCATCTTTT
1 ACAAATCAACATTT
67223 ACAAATCAA
1 ACAAATCAA
67232 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:68682 original size:42 final size:42
Alignment explanation
Indices: 68578--68686 Score: 114
Period size: 42 Copynumber: 2.6 Consensus size: 42
68568 AGAATGTTGG
* * * *
68578 GAGGGACCTCTTCAACGATGACAGTGGCCTCTTGAACGGTGT
1 GAGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGATGT
* ** *
68620 GAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGATAG-
1 GAGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGAT-GT
68662 G-GGAGGCCTCTTGAACGATGACAGG
1 GAGG-GGCCTCTTGAACGATGACAGG
68687 TGAGTCGGGC
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
41 2 0.04
42 50 0.94
43 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.21
Consensus pattern (42 bp):
GAGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGATGT
Found at i:69229 original size:20 final size:20
Alignment explanation
Indices: 69166--69319 Score: 102
Period size: 20 Copynumber: 8.3 Consensus size: 20
69156 GAAACTTAAA
*
69166 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
69186 ATCAAAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
69206 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
*
69226 ATCGCAA--CG-AGA-GA--
1 ATCGCAATGCGAAAATGACT
**
69240 ATCGCAATGCG-AAATGAAA
1 ATCGCAATGCGAAAATGACT
69259 ATCGCAA--C-AACAA--A--
1 ATCGCAATGCGAA-AATGACT
*
69273 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
69293 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
69313 ATCGCAA
1 ATCGCAA
69320 CGAGAGAATC
Statistics
Matches: 107, Mismatches: 13, Indels: 28
0.72 0.09 0.19
Matches are distributed among these distances:
14 14 0.13
16 10 0.09
17 7 0.07
18 5 0.05
19 7 0.07
20 64 0.60
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.18
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:69249 original size:34 final size:33
Alignment explanation
Indices: 69206--69299 Score: 107
Period size: 34 Copynumber: 2.8 Consensus size: 33
69196 GAAAATGACT
* * * *
69206 ATCGCAATGCGAATTTGACTATCGCAACGAGAGA
1 ATCGCAATGCGAA-ATGACTATCGCAACAACAAA
**
69240 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
1 ATCGCAATGCGAAATGACTATCGCAACAACAAA
*
69273 ATCGCAACGCGAAAATGACTATCGCAA
1 ATCGCAATGCG-AAATGACTATCGCAA
69300 TGCGAATTTG
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 24 0.48
34 26 0.52
ACGTcount: A:0.43, C:0.22, G:0.19, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGACTATCGCAACAACAAA
Found at i:69276 original size:33 final size:33
Alignment explanation
Indices: 69206--69286 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 33
69196 GAAAATGACT
* ** * * *
69206 ATCGCAATGCGAATTTGACTATCGCAACGAGAGA
1 ATCGCAATGCGAA-ATGAAAATCGCAACAACAAA
69240 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
*
69273 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
69287 ATGACTATCG
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 27 0.68
34 13 0.32
ACGTcount: A:0.43, C:0.22, G:0.20, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACAACAAA
Found at i:69444 original size:20 final size:20
Alignment explanation
Indices: 69366--69504 Score: 156
Period size: 20 Copynumber: 7.5 Consensus size: 20
69356 GATTCTTTCG
**
69366 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
69386 TTGCAATAGTCATTTT--CA
1 TTGCGATAGTCATTTTCGCA
69404 TTGCGATAGTCA-TTT--CA
1 TTGCGATAGTCATTTTCGCA
69421 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
69441 TTGCGAT--TC-TCTT-G--
1 TTGCGATAGTCATTTTCGCA
*
69455 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
69475 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
69495 TTGCGATAGT
1 TTGCGATAGT
69505 AAACTATTCT
Statistics
Matches: 103, Mismatches: 7, Indels: 18
0.80 0.05 0.14
Matches are distributed among these distances:
14 7 0.07
16 3 0.03
17 23 0.22
18 19 0.18
20 51 0.50
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:71376 original size:20 final size:20
Alignment explanation
Indices: 71353--71438 Score: 77
Period size: 20 Copynumber: 4.4 Consensus size: 20
71343 CTGAAACTTT
71353 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
*
71373 AAATCGCAACACAAAAATGA
1 AAATCGCAACACGAAAATGA
** * **
71393 CTATCGCAACGCGAATTTGA
1 AAATCGCAACACGAAAATGA
** *
71413 CTATCGCAACGCG--AATGA
1 AAATCGCAACACGAAAATGA
71431 AAATCGCA
1 AAATCGCA
71439 TTGCGATTCT
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
18 9 0.16
20 46 0.84
ACGTcount: A:0.45, C:0.23, G:0.16, T:0.15
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:71478 original size:20 final size:20
Alignment explanation
Indices: 71453--71499 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
71443 GATTCTCTCG
71453 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
71473 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
71493 TTGCGAT
1 TTGCGAT
71500 TCACTCGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:72103 original size:20 final size:20
Alignment explanation
Indices: 72080--72148 Score: 120
Period size: 20 Copynumber: 3.5 Consensus size: 20
72070 AGTCAGATTT
72080 GCATTGCGATTTACGTATTC
1 GCATTGCGATTTACGTATTC
*
72100 GCATTGCGATTTACGTAATC
1 GCATTGCGATTTACGTATTC
*
72120 GCGTTGCGATTTACGTATTC
1 GCATTGCGATTTACGTATTC
72140 GCATTGCGA
1 GCATTGCGA
72149 ATCAGGAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.36
Consensus pattern (20 bp):
GCATTGCGATTTACGTATTC
Done.