Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008180.1 Hibiscus syriacus cultivar Beakdansim tig00110777_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: 2670214
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 14
Found at i:2588123 original size:201 final size:201
Alignment explanation
Indices: 2587773--2588168 Score: 749
Period size: 201 Copynumber: 2.0 Consensus size: 201
2587763 ATATGAGAAT
*
2587773 TGTAATAACATATTAGATAAATTATACTATTCATCACTCAACTATTTTTTTACTCCTATTTTAGT
1 TGTAATAACATATTAGATAAATTATACTATTCATCACTCAACTATCTTTTTACTCCTATTTTAGT
2587838 CACTAATTTTTTTTTTAATTTAATCACTCAATTTCAAACATTGAATTTTTAGTCACCCTATCGTT
66 CACTAA-TTTTTTTTTAATTTAATCACTCAATTTCAAACATTGAATTTTTAGTCACCCTATCGTT
2587903 TTCTCTGTACCACCGTGATGATATGACTTTTTTTAATTAATTTTCAAACTGCCATATAAGTCCCA
130 TTCTCTGTACCACCGTGATGATATGAC-TTTTTTAATTAATTTTCAAACTGCCATATAAGTCCCA
2587968 AAAAAAAG
194 AAAAAAAG
*
2587976 TGTAATAACATATTAGATAAATTATACTATTCATCACTCAACTATCTTTTTACTCTTATTTTAGT
1 TGTAATAACATATTAGATAAATTATACTATTCATCACTCAACTATCTTTTTACTCCTATTTTAGT
2588041 CACTAA-TTTTTTTTAATTTAATCACTCAATTTCAAACATTGAATTTTTAGTCACCCTATCGTTT
66 CACTAATTTTTTTTTAATTTAATCACTCAATTTCAAACATTGAATTTTTAGTCACCCTATCGTTT
2588105 TCTCTGTACCACCGTGATGATATGACTTTTTTAATTAATTTTCAAACTGCCATATAAGTCCCAA
131 TCTCTGTACCACCGTGATGATATGACTTTTTTAATTAATTTTCAAACTGCCATATAAGTCCCAA
2588169 TAAATATTTT
Statistics
Matches: 191, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
200 38 0.20
201 84 0.44
203 69 0.36
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (201 bp):
TGTAATAACATATTAGATAAATTATACTATTCATCACTCAACTATCTTTTTACTCCTATTTTAGT
CACTAATTTTTTTTTAATTTAATCACTCAATTTCAAACATTGAATTTTTAGTCACCCTATCGTTT
TCTCTGTACCACCGTGATGATATGACTTTTTTAATTAATTTTCAAACTGCCATATAAGTCCCAAA
AAAAAG
Found at i:2592204 original size:364 final size:364
Alignment explanation
Indices: 2591535--2592262 Score: 1402
Period size: 364 Copynumber: 2.0 Consensus size: 364
2591525 AAATGAAGCA
2591535 TTTTCAGATAATTAAAGGAAACTTTTTATGTTAGCAAATGTGTGATTCCTTTTTTAAAAAAATTT
1 TTTTCAGATAATTAAAGGAAACTTTTTATGTTAGCAAATGTGTGATTCCTTTTTTAAAAAAATTT
2591600 AATTCTCTAGAAAAACTTCAGAATCCACCTTTGGGATTTAGTTGATTTTGTTTCTGATATGCTAA
66 AATTCTCTAGAAAAACTTCAGAATCCACCTTTGGGATTTAGTTGATTTTGTTTCTGATATGCTAA
2591665 AATGAGTGACCTCTTTAATTTTCGTATTATTTCCTATTTTTCTTTTTTTTTCAACTGATTTATAC
131 AATGAGTGACCTCTTTAATTTTCGTATTATTTCCTATTTTTCTTTTTTTTTCAACTGATTTATAC
2591730 AAAAGGAGTGATAGTTTTTCCTCCTTTTTCTATTTTAATATCTAATTTTTGGAGTTTAGATCAAA
196 AAAAGGAGTGATAGTTTTTCCTCCTTTTTCTATTTTAATATCTAATTTTTGGAGTTTAGATCAAA
2591795 CTTGAATCTATAGGTTTTTTCAGTGTGTTGACTTTTGATTTTAGATTTCTCCATAGTTGTTTATA
261 CTTGAATCTATAGGTTTTTTCAGTGTGTTGACTTTTGATTTTAGATTTCTCCATAGTTGTTTATA
*
2591860 ATATGCTAATTGTTTCTATTTCTATTGAATTTTGCAGTT
326 ATATGCTAATTATTTCTATTTCTATTGAATTTTGCAGTT
****
2591899 TTTTCAGATAATTAAAGGAAACTTTTTATGTTAGCAAATGTGTGATTCCTTTTTTTTTTAAATTT
1 TTTTCAGATAATTAAAGGAAACTTTTTATGTTAGCAAATGTGTGATTCCTTTTTTAAAAAAATTT
2591964 AATTCTCTAGAAAAACTTCAGAATCCACCTTTGGGATTTAGTTGATTTTGTTTCTGATATGCTAA
66 AATTCTCTAGAAAAACTTCAGAATCCACCTTTGGGATTTAGTTGATTTTGTTTCTGATATGCTAA
2592029 AATGAGTGACCTCTTTAATTTTCGTATTATTTCCTATTTTTCTTTTTTTTTCAACTGATTTATAC
131 AATGAGTGACCTCTTTAATTTTCGTATTATTTCCTATTTTTCTTTTTTTTTCAACTGATTTATAC
*
2592094 AAAAGGAGTGATAGTTTTTCCTCCTTTTTCTTTTTTAATATCTAATTTTTGGAGTTTAGATCAAA
196 AAAAGGAGTGATAGTTTTTCCTCCTTTTTCTATTTTAATATCTAATTTTTGGAGTTTAGATCAAA
2592159 CTTGAATCTATAGGTTTTTTCAGTGTGTTGACTTTTGATTTTAGATTTCTCCATAGTTGTTTATA
261 CTTGAATCTATAGGTTTTTTCAGTGTGTTGACTTTTGATTTTAGATTTCTCCATAGTTGTTTATA
2592224 ATATGCTAATTATTTCTATTTCTATTGAATTTTGCAGTT
326 ATATGCTAATTATTTCTATTTCTATTGAATTTTGCAGTT
2592263 AAGATTTGAA
Statistics
Matches: 358, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
364 358 1.00
ACGTcount: A:0.26, C:0.12, G:0.13, T:0.49
Consensus pattern (364 bp):
TTTTCAGATAATTAAAGGAAACTTTTTATGTTAGCAAATGTGTGATTCCTTTTTTAAAAAAATTT
AATTCTCTAGAAAAACTTCAGAATCCACCTTTGGGATTTAGTTGATTTTGTTTCTGATATGCTAA
AATGAGTGACCTCTTTAATTTTCGTATTATTTCCTATTTTTCTTTTTTTTTCAACTGATTTATAC
AAAAGGAGTGATAGTTTTTCCTCCTTTTTCTATTTTAATATCTAATTTTTGGAGTTTAGATCAAA
CTTGAATCTATAGGTTTTTTCAGTGTGTTGACTTTTGATTTTAGATTTCTCCATAGTTGTTTATA
ATATGCTAATTATTTCTATTTCTATTGAATTTTGCAGTT
Found at i:2600926 original size:168 final size:171
Alignment explanation
Indices: 2600633--2600942 Score: 536
Period size: 168 Copynumber: 1.8 Consensus size: 171
2600623 ACAAACACTA
** **
2600633 ACAAACATGTTTAAAAACAAATAAATGAACATGAATATGATATTAAAAATTTAAACGAACACGAA
1 ACAAACACCTTTAAAAACAAATAAATGAACACAAATATGATATTAAAAATTTAAACGAACAC-AA
* *
2600698 TTTAACATAAACATCTTTAAAAATAAATCGAACATAAGCACAAACTTATTCATTCAAACTTGGTT
65 TTGAACATAAACATCTTTAAAAATAAATCGAACACAAGCACAAACTTATTCATTCAAACTTGGTT
2600763 CATTTACACCCCCACTCAACTTCAAACACTAAAGTAACAGAC
130 CATTTACACCCCCACTCAACTTCAAACACTAAAGTAACAGAC
2600805 ACAAACACCTTTAAAAACAAATAAATGAACACAAATATGATATTAAAAATTTAAACG-A-AC-AT
1 ACAAACACCTTTAAAAACAAATAAATGAACACAAATATGATATTAAAAATTTAAACGAACACAAT
2600867 TGAACATAAACATCTTTAAAAATAAATCGAACACAAGCACAAACTTATTCATTCAAACTTGGTTC
66 TGAACATAAACATCTTTAAAAATAAATCGAACACAAGCACAAACTTATTCATTCAAACTTGGTTC
2600932 ATTTACACCCC
131 ATTTACACCCC
2600943 ACGAAAAGCT
Statistics
Matches: 132, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
168 76 0.58
170 2 0.02
171 1 0.01
172 53 0.40
ACGTcount: A:0.49, C:0.19, G:0.06, T:0.25
Consensus pattern (171 bp):
ACAAACACCTTTAAAAACAAATAAATGAACACAAATATGATATTAAAAATTTAAACGAACACAAT
TGAACATAAACATCTTTAAAAATAAATCGAACACAAGCACAAACTTATTCATTCAAACTTGGTTC
ATTTACACCCCCACTCAACTTCAAACACTAAAGTAACAGAC
Found at i:2601070 original size:22 final size:23
Alignment explanation
Indices: 2601045--2601088 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2601035 AAACATTTTA
* *
2601045 AAACTT-AGCTCAATTGAAGCTC
1 AAACTTGAGCACAATTCAAGCTC
2601067 AAACTTGAGCACAATTCAAGCT
1 AAACTTGAGCACAATTCAAGCT
2601089 AGAACTCAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.25
Consensus pattern (23 bp):
AAACTTGAGCACAATTCAAGCTC
Found at i:2603352 original size:25 final size:25
Alignment explanation
Indices: 2603318--2603374 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
2603308 TGAATCGGAT
*
2603318 TTTTTTTTATTAATTAATTGATTAA
1 TTTTTTTTATTAATTAATCGATTAA
2603343 TTTTTTTTATTAATTAATCGATTAA
1 TTTTTTTTATTAATTAATCGATTAA
2603368 TTTTTTT
1 TTTTTTT
2603375 ATCCAGTCGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (25 bp):
TTTTTTTTATTAATTAATCGATTAA
Found at i:2614951 original size:399 final size:399
Alignment explanation
Indices: 2614213--2615010 Score: 1587
Period size: 399 Copynumber: 2.0 Consensus size: 399
2614203 CAATCATGCA
2614213 TTCCATTATATTTTACTTCTTTGTATCGGTATGGCTTTAGGGTATCAATCCTGTAGAATCAAAAT
1 TTCCATTATATTTTACTTCTTTGTATCGGTATGGCTTTAGGGTATCAATCCTGTAGAATCAAAAT
2614278 AGAGTAAAAACTCTAATTGATTGAGAAAAAGAAAATCTCTTTAGAATAATCTCATAAAATTGCAA
66 AGAGTAAAAACTCTAATTGATTGAGAAAAAGAAAATCTCTTTAGAATAATCTCATAAAATTGCAA
2614343 AAGGGAAGAACTCTTAAGAAAGCTTTCAAATGCTTATAATTAAGCTTTGATTGTTGGATGATAAA
131 AAGGGAAGAACTCTTAAGAAAGCTTTCAAATGCTTATAATTAAGCTTTGATTGTTGGATGATAAA
2614408 ACTCAAATACAAGTAGGGTATTTATAGGTTACAAGAAACAATCTAAACCACTCATTAAAATAATC
196 ACTCAAATACAAGTAGGGTATTTATAGGTTACAAGAAACAATCTAAACCACTCATTAAAATAATC
2614473 ACTAAATAATCTAAACCATTGAAATTAAAACATGAGAAAAATACTTAATTTTCACCTAACTAAAT
261 ACTAAATAATCTAAACCATTGAAATTAAAACATGAGAAAAATACTTAATTTTCACCTAACTAAAT
2614538 TGATGTAAGCAATGACATCAAATTAATTTAGGTATGAACTTATTTAGGCTAATATTGAATTTTCA
326 TGATGTAAGCAATGACATCAAATTAATTTAGGTATGAACTTATTTAGGCTAATATTGAATTTTCA
2614603 ACACTCCCC
391 ACACTCCCC
2614612 TTCCATTATATTTTACTTCTTTGTATCGGTATGGCTTTAGGGTATCAATCCTGTAGAATCAAAAT
1 TTCCATTATATTTTACTTCTTTGTATCGGTATGGCTTTAGGGTATCAATCCTGTAGAATCAAAAT
*
2614677 AGAGTAAAAACTCTAATTGATTGAGAAGAAGAAAATCTCTTTAGAATAATCTCATAAAATTGCAA
66 AGAGTAAAAACTCTAATTGATTGAGAAAAAGAAAATCTCTTTAGAATAATCTCATAAAATTGCAA
2614742 AAGGGAAGAACTCTTAAGAAAGCTTTCAAATGCTTATAATTAAGCTTTGATTGTTGGATGATAAA
131 AAGGGAAGAACTCTTAAGAAAGCTTTCAAATGCTTATAATTAAGCTTTGATTGTTGGATGATAAA
2614807 ACTCAAATACAAGTAGGGTATTTATAGGTTACAAGAAACAATCTAAACCACTCATTAAAATAATC
196 ACTCAAATACAAGTAGGGTATTTATAGGTTACAAGAAACAATCTAAACCACTCATTAAAATAATC
2614872 ACTAAATAATCTAAACCATTGAAATTAAAACATGAGAAAAATACTTAATTTTCACCTAACTAAAT
261 ACTAAATAATCTAAACCATTGAAATTAAAACATGAGAAAAATACTTAATTTTCACCTAACTAAAT
2614937 TGATGTAAGCAATGACATCAAATTAATTTAGGTATGAACTTATTTAGGCTAATATTGAATTTTCA
326 TGATGTAAGCAATGACATCAAATTAATTTAGGTATGAACTTATTTAGGCTAATATTGAATTTTCA
2615002 ACACTCCCC
391 ACACTCCCC
2615011 CTCAATGTTA
Statistics
Matches: 398, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
399 398 1.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (399 bp):
TTCCATTATATTTTACTTCTTTGTATCGGTATGGCTTTAGGGTATCAATCCTGTAGAATCAAAAT
AGAGTAAAAACTCTAATTGATTGAGAAAAAGAAAATCTCTTTAGAATAATCTCATAAAATTGCAA
AAGGGAAGAACTCTTAAGAAAGCTTTCAAATGCTTATAATTAAGCTTTGATTGTTGGATGATAAA
ACTCAAATACAAGTAGGGTATTTATAGGTTACAAGAAACAATCTAAACCACTCATTAAAATAATC
ACTAAATAATCTAAACCATTGAAATTAAAACATGAGAAAAATACTTAATTTTCACCTAACTAAAT
TGATGTAAGCAATGACATCAAATTAATTTAGGTATGAACTTATTTAGGCTAATATTGAATTTTCA
ACACTCCCC
Found at i:2617680 original size:31 final size:31
Alignment explanation
Indices: 2617642--2617797 Score: 269
Period size: 31 Copynumber: 5.0 Consensus size: 31
2617632 GGGGTCGAGG
*
2617642 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2617673 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
2617704 GTTTACCTATGTTCTTCGGGACATATGAACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2617735 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
2617766 GTTTACCTAGGTTCTTCGGGATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
2617797 G
1 G
2617798 GTCCTTTGGG
Statistics
Matches: 120, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 119 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:2620946 original size:64 final size:64
Alignment explanation
Indices: 2620864--2621020 Score: 183
Period size: 64 Copynumber: 2.5 Consensus size: 64
2620854 TTGAAGGTGT
* * *** *
2620864 ATCGATGCACAAGAAGTGCATCGATGCA-CTCTTTTAA-AATAAAAACATCGAATGCAATTCATG
1 ATCGATGCATAAGTAGTGCATCGATGCATC-CCAGTAATAAT-AAAACATCGAATACAATTCATG
2620927 C
64 C
* * *
2620928 ATCGATGCATAAGTAGTGCATCGATGCATCCCAGTAATAATACAACATCGAATACATTTTATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCAGTAATAATAAAACATCGAATACAATTCATGC
* *
2620992 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAGTGCATCGATGCAT
2621021 ACTTTCATTA
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
64 76 0.95
65 4 0.05
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCAGTAATAATAAAACATCGAATACAATTCATGC
Found at i:2621728 original size:31 final size:31
Alignment explanation
Indices: 2621635--2621717 Score: 141
Period size: 31 Copynumber: 2.7 Consensus size: 31
2621625 AGGGTCGAGG
2621635 GTTTACCTATGTTCTTCGGGACATATGGA-T
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2621665 CGTTTACCTATGTTCTTCGGGACATATGGACT
1 -GTTTACCTATGTTCTTCGGGACATATGGACT
*
2621697 GTTTACCTAGGTTCTTCGGGA
1 GTTTACCTATGTTCTTCGGGA
2621718 TCTAGGGACT
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
31 49 0.98
32 1 0.02
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:2625968 original size:29 final size:29
Alignment explanation
Indices: 2625926--2625984 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2625916 ATTTTCACCT
2625926 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
2625955 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
2625984 A
1 A
2625985 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:2629515 original size:36 final size:36
Alignment explanation
Indices: 2629460--2629539 Score: 117
Period size: 36 Copynumber: 2.2 Consensus size: 36
2629450 CCCATTCCTA
* *
2629460 TTTTC-AACAAACATCTACCAAACTTTGAAAAACAT
1 TTTTCAAAGAAACATCTACCAAACTTTAAAAAACAT
* *
2629495 TTTTCAAAGAAACATTTACCAAACTTTAAAAAATAT
1 TTTTCAAAGAAACATCTACCAAACTTTAAAAAACAT
2629531 TTTTCAAAG
1 TTTTCAAAG
2629540 TTGGTTGCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 5 0.12
36 35 0.88
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (36 bp):
TTTTCAAAGAAACATCTACCAAACTTTAAAAAACAT
Found at i:2632839 original size:15 final size:15
Alignment explanation
Indices: 2632819--2632850 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2632809 AAAATATTTC
*
2632819 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTGGAT
2632834 TTTCCCGTTCTGGAT
1 TTTCCCGTTCTGGAT
2632849 TT
1 TT
2632851 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.25, G:0.16, T:0.53
Consensus pattern (15 bp):
TTTCCCGTTCTGGAT
Found at i:2634089 original size:21 final size:21
Alignment explanation
Indices: 2634065--2634133 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
2634055 CAAACTTTAC
2634065 CAAACTTTGAAAAACATTTTT
1 CAAACTTTGAAAAACATTTTT
* * **
2634086 CAAATTTTCAAAGAAACATTTAC
1 CAAACTTT-GAA-AAACATTTTT
2634109 CAAACTTTGAAAAACATTTTT
1 CAAACTTTGAAAAACATTTTT
2634130 CAAA
1 CAAA
2634134 GTTGGTTGCC
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
21 19 0.50
22 4 0.11
23 15 0.39
ACGTcount: A:0.46, C:0.16, G:0.04, T:0.33
Consensus pattern (21 bp):
CAAACTTTGAAAAACATTTTT
Found at i:2634590 original size:22 final size:22
Alignment explanation
Indices: 2634565--2634613 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
2634555 AGTTGTAGTA
2634565 TTTTCCTAATTGAGTTGTAACT-
1 TTTTCCTAATTGAGTTG-AACTC
** *
2634587 TTTTTTTAATTGTGTTGAACTC
1 TTTTCCTAATTGAGTTGAACTC
2634609 TTTTC
1 TTTTC
2634614 TTCAATATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.18, C:0.12, G:0.12, T:0.57
Consensus pattern (22 bp):
TTTTCCTAATTGAGTTGAACTC
Found at i:2634607 original size:21 final size:22
Alignment explanation
Indices: 2634571--2634612 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2634561 AGTATTTTCC
*
2634571 TAATTGAGTTGTAACTTTTTTT
1 TAATTGAGTTGTAACTCTTTTT
*
2634593 TAATTGTGTTG-AACTCTTTT
1 TAATTGAGTTGTAACTCTTTT
2634613 CTTCAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.57
Consensus pattern (22 bp):
TAATTGAGTTGTAACTCTTTTT
Found at i:2637694 original size:21 final size:21
Alignment explanation
Indices: 2637668--2637712 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2637658 GATTTCTGGG
* *
2637668 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2637689 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2637710 CAA
1 CAA
2637713 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2639470 original size:23 final size:22
Alignment explanation
Indices: 2639411--2639477 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
2639401 TATGGACATC
*
2639411 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
2639433 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
2639455 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
2639478 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:2642645 original size:21 final size:21
Alignment explanation
Indices: 2642619--2642663 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2642609 GATTTCTGGG
* *
2642619 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2642640 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2642661 CAA
1 CAA
2642664 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2644418 original size:23 final size:22
Alignment explanation
Indices: 2644359--2644425 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
2644349 TATGGACATC
*
2644359 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
2644381 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
2644403 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
2644426 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:2645427 original size:17 final size:18
Alignment explanation
Indices: 2645398--2645432 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
2645388 CTACAAAATG
2645398 TAATATGTAAATTAATAA
1 TAATATGTAAATTAATAA
2645416 TAATAT-TAAATTAATAA
1 TAATATGTAAATTAATAA
2645433 AATGTAGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
TAATATGTAAATTAATAA
Found at i:2654683 original size:24 final size:24
Alignment explanation
Indices: 2654625--2654683 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
2654615 TCTCAGCTCT
*
2654625 AAGGATGTTGATGAAAAGGTTGAG
1 AAGGATGTTGATGAAAAGGTTAAG
**
2654649 AAGGACATTGATGAAAAGGTTAAG
1 AAGGATGTTGATGAAAAGGTTAAG
2654673 AAGGATGTTGA
1 AAGGATGTTGA
2654684 GGCTGATGCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.41, C:0.02, G:0.34, T:0.24
Consensus pattern (24 bp):
AAGGATGTTGATGAAAAGGTTAAG
Found at i:2658025 original size:23 final size:23
Alignment explanation
Indices: 2657981--2658025 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
2657971 CAAATAGTCA
* * **
2657981 TTTTGTTATGTATTTTTTTTTTC
1 TTTTGTGAAGTATTTTAATTTTC
2658004 TTTTGTGAAGTATTTTAATTTT
1 TTTTGTGAAGTATTTTAATTTT
2658026 TGGTCAAAAC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.16, C:0.02, G:0.11, T:0.71
Consensus pattern (23 bp):
TTTTGTGAAGTATTTTAATTTTC
Found at i:2667049 original size:38 final size:38
Alignment explanation
Indices: 2667001--2667082 Score: 128
Period size: 38 Copynumber: 2.2 Consensus size: 38
2666991 CACAAAGTAT
*
2667001 AGGAGACTGCAGTAAGGACTTACCCTGAGCACAAAGCG
1 AGGAGCCTGCAGTAAGGACTTACCCTGAGCACAAAGCG
**
2667039 AGGAGCCTGCAGTAAGGACTTATTCTGAGCACAAAGCG
1 AGGAGCCTGCAGTAAGGACTTACCCTGAGCACAAAGCG
*
2667077 ATGAGC
1 AGGAGC
2667083 TTACGGAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.33, C:0.22, G:0.29, T:0.16
Consensus pattern (38 bp):
AGGAGCCTGCAGTAAGGACTTACCCTGAGCACAAAGCG
Found at i:2668847 original size:58 final size:58
Alignment explanation
Indices: 2668695--2668855 Score: 152
Period size: 58 Copynumber: 2.7 Consensus size: 58
2668685 GGATGAATTA
* ** *
2668695 AGGATGAAATTAGAA-ATTCAAAGTTTGGAGA-CTAAATTAGAAA-GAGGGTCATAGTTTAG
1 AGGATGAAATTAGAATATTCAAAATTTAAAGATC-AATTTA-AAACGA--GTCATAGTTTAG
* *
2668754 GGGATGAAATTAGAATGTTCAAAATTTCAAAGATCAATTTAAAACGAGTCATAGTTT-G
1 AGGATGAAATTAGAATATTCAAAATTT-AAAGATCAATTTAAAACGAGTCATAGTTTAG
* *
2668812 AGTATGAAATTAGAATATTCAAAAAGTTT-AGGATCAATTTAAAA
1 AGGATGAAATTAGAATATTC-AAAA-TTTAAAGATCAATTTAAAA
2668856 TGAGGGTATA
Statistics
Matches: 86, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
58 32 0.37
59 28 0.33
60 15 0.17
61 10 0.12
62 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.20, T:0.30
Consensus pattern (58 bp):
AGGATGAAATTAGAATATTCAAAATTTAAAGATCAATTTAAAACGAGTCATAGTTTAG
Found at i:2669748 original size:115 final size:115
Alignment explanation
Indices: 2669569--2669904 Score: 421
Period size: 115 Copynumber: 2.9 Consensus size: 115
2669559 TATTTACAAA
* *
2669569 TTTAAGAAAGACACG-CCAACAAT-ATGATCTTTCTAGTCTCCACCCAA-TGTTATTTACGTGTT
1 TTTAAAAAAGACACGAACAAC-ATCAT-ATCTTTCTAGTCTCCACCCAATTGTTATTTACGTGTT
*
2669631 TTTCTTAAAATCATCATACAATCTAATAATTTTTTCAAAATTACATGACGAT
64 TTTCTTAAAATCATCATACAATCTAATAATTTTTTCAAAATTACAGGACGAT
* * * * **
2669683 TTTAAAAAAGACACGTTATAATATGATATCTTTCTAGTCTCCACCCAATTGTTATTT-CGCCTTT
1 TTTAAAAAAGACACG-AACAACATCATATCTTTCTAGTCTCCACCCAATTGTTATTTACGTGTTT
* *
2669747 TTCTTAAAATCATCAAACAATCTAATAATTTTTTCAAAATTATAGGACGAT
65 TTCTTAAAATCATCATACAATCTAATAATTTTTTCAAAATTACAGGACGAT
* * * *
2669798 TTTAAGAAAGACACGAACAACATCAT-TCTTTATAGTCTCCACTCAATTGTTGTTTACGTGTTTT
1 TTTAAAAAAGACACGAACAACATCATATCTTTCTAGTCTCCACCCAATTGTTATTTACGTGTTTT
* * * *
2669862 TCTTAAAGTCATCCTATAATCTAATCATTTTTTCCAAACATTA
66 TCTTAAAATCATCATACAATCTAATAATTTTTT-CAAA-ATTA
2669905 TAAATATCAT
Statistics
Matches: 191, Mismatches: 24, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
113 26 0.14
114 55 0.29
115 94 0.49
116 16 0.08
ACGTcount: A:0.34, C:0.19, G:0.08, T:0.39
Consensus pattern (115 bp):
TTTAAAAAAGACACGAACAACATCATATCTTTCTAGTCTCCACCCAATTGTTATTTACGTGTTTT
TCTTAAAATCATCATACAATCTAATAATTTTTTCAAAATTACAGGACGAT
Done.