Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003546.1 Hibiscus syriacus cultivar Beakdansim tig00007478_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: 106515
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:3943 original size:2 final size:2
Alignment explanation
Indices: 3936--4000 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
3926 AACATCTACA
*
3936 AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3978 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
4001 GTTTGGATTG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6811 original size:241 final size:239
Alignment explanation
Indices: 6387--6866 Score: 890
Period size: 241 Copynumber: 2.0 Consensus size: 239
6377 ATATCAATAT
6387 CGGTGCTTCATATATGAAGTATTAAAACCATTAAGTGGCTGCTATAGAATTCCTATTTCTTCCAC
1 CGGTGCTTCATATATGAAGTATTAAAACCATTAAGTGGCTGCTATAGAATTCC-ATTTCTTCCAC
*
6452 CAGCTAGCCAAAAAAATTCATGCATGAATAAGCCAACCATGGATGTTATGACAACAATTTGGAAA
65 CAGCTAGCCAAAAAAATTCATGCATGAATAAGCCAACCATAGATGTTATGACAACAATTTGGAAA
6517 ATTACAGGTCTGAGCCTTACAGTGTCAATGAGATTTCTAGGTGTGGAAAGGACGGCACCGCTATG
130 ATTACAGGTCTGAGCCTTACAGTGTCAATGAGATTTCTAGGTGTGGAAAGGACGGCACCGCTATG
6582 GTAGTAATCTATCCCCAAACCACCTCCAATGTTCAAATAATCAAC
195 GTAGTAATCTATCCCCAAACCACCTCCAATGTTCAAATAATCAAC
6627 CGGTGCTTCATATATGAAGTATTAAAAAACCATTAAGTGGCTGCTATAGAATTCC-TTTCTTCCA
1 CGGTGCTTCATATATGAAGTATT--AAAACCATTAAGTGGCTGCTATAGAATTCCATTTCTTCCA
6691 CCAGCTAGCCAAAAACAATTCATGCATGAATAAGCCAACCATAGATGTTATGACAACAATTTGGA
64 CCAGCTAGCCAAAAA-AATTCATGCATGAATAAGCCAACCATAGATGTTATGACAACAATTTGGA
* *
6756 AAATTAGAGGTCTGAGCCTTACAGTGTCAATGAGATTTCTAGGTGTGGGAAGGACGGCACCGCTA
128 AAATTACAGGTCTGAGCCTTACAGTGTCAATGAGATTTCTAGGTGTGGAAAGGACGGCACCGCTA
6821 TGGTAGTAATCTATCCCCAAACCACCTCCAATGTTCAAATAATCAA
193 TGGTAGTAATCTATCCCCAAACCACCTCCAATGTTCAAATAATCAA
6867 TTTCAAACCC
Statistics
Matches: 234, Mismatches: 3, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
240 47 0.20
241 157 0.67
242 30 0.13
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (239 bp):
CGGTGCTTCATATATGAAGTATTAAAACCATTAAGTGGCTGCTATAGAATTCCATTTCTTCCACC
AGCTAGCCAAAAAAATTCATGCATGAATAAGCCAACCATAGATGTTATGACAACAATTTGGAAAA
TTACAGGTCTGAGCCTTACAGTGTCAATGAGATTTCTAGGTGTGGAAAGGACGGCACCGCTATGG
TAGTAATCTATCCCCAAACCACCTCCAATGTTCAAATAATCAAC
Found at i:10698 original size:2 final size:2
Alignment explanation
Indices: 10691--10717 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10681 AACCTAATTA
10691 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
10718 CTTCTACATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11666 original size:28 final size:27
Alignment explanation
Indices: 11631--11692 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 27
11621 CAGATTATTT
*
11631 TATTAT-TTTT-ATATGATGTGATATA
1 TATTATATTTTAATATGATATGATATA
*
11656 TATTAATATTTTAATATGATATGTTATA
1 TATT-ATATTTTAATATGATATGATATA
11684 TATTATATT
1 TATTATATT
11693 AATAGTGCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 4 0.12
26 2 0.06
27 9 0.28
28 17 0.53
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.56
Consensus pattern (27 bp):
TATTATATTTTAATATGATATGATATA
Found at i:26292 original size:16 final size:17
Alignment explanation
Indices: 26271--26304 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
26261 ATGATATAAA
*
26271 ATATATTTTTAAA-ATT
1 ATATATTATTAAATATT
26287 ATATATTATTAAATATT
1 ATATATTATTAAATATT
26304 A
1 A
26305 AAATAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATATTATTAAATATT
Found at i:26633 original size:16 final size:15
Alignment explanation
Indices: 26591--26634 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
26581 TCAAATTTAT
26591 TTATTTTTAAAA-AA
1 TTATTTTTAAAATAA
*
26605 TTATTTATCAAAATAA
1 TTATTT-TTAAAATAA
26621 TTAGTTTTTAAAAT
1 TTA-TTTTTAAAAT
26635 TATATATACC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 6 0.24
15 5 0.20
16 11 0.44
17 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (15 bp):
TTATTTTTAAAATAA
Found at i:32861 original size:21 final size:21
Alignment explanation
Indices: 32837--32906 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
32827 TATGAACATG
32837 TGAATTATATGAAAAGTGATA
1 TGAATTATATGAAAAGTGATA
* * *
32858 TGAATTACATGAAAAGAAGCTA
1 TGAATTATATGAAAAG-TGATA
* *
32880 TGAGCTTATATGAACATGTGATA
1 TGA-ATTATATGAA-AAGTGATA
32903 TGAA
1 TGAA
32907 AGTGTATATG
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
21 15 0.41
22 6 0.16
23 14 0.38
24 2 0.05
ACGTcount: A:0.44, C:0.06, G:0.20, T:0.30
Consensus pattern (21 bp):
TGAATTATATGAAAAGTGATA
Found at i:33442 original size:2 final size:2
Alignment explanation
Indices: 33437--33467 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
33427 TATATATATA
33437 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
33468 TATATTGCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:38713 original size:6 final size:6
Alignment explanation
Indices: 38702--38732 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
38692 CACAACACAA
38702 CACATT CACATT CACATT CACATT CACATT C
1 CACATT CACATT CACATT CACATT CACATT C
38733 CCCAATTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.32
Consensus pattern (6 bp):
CACATT
Found at i:46526 original size:19 final size:20
Alignment explanation
Indices: 46464--46514 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
46454 GGCTTTCGAG
* *
46464 TATCTATACTCCCTGAATA-A
1 TATCGATAC-CCCTAAATATA
46484 TATCGATACCCCTAAATATA
1 TATCGATACCCCTAAATATA
46504 TATCGATACCC
1 TATCGATACCC
46515 TATCATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 8 0.29
20 20 0.71
ACGTcount: A:0.35, C:0.27, G:0.06, T:0.31
Consensus pattern (20 bp):
TATCGATACCCCTAAATATA
Found at i:54764 original size:15 final size:15
Alignment explanation
Indices: 54755--54787 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
54745 CTTCTTTCTT
54755 TTTCTTTTCTGTTTC
1 TTTCTTTTCTGTTTC
54770 TTTCTTTTCTGTTTC
1 TTTCTTTTCTGTTTC
54785 TTT
1 TTT
54788 GTATCTCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.18, G:0.06, T:0.76
Consensus pattern (15 bp):
TTTCTTTTCTGTTTC
Found at i:54771 original size:21 final size:21
Alignment explanation
Indices: 54746--54785 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
54736 TAAGTTTCTC
54746 TTCTTTCTTTTTCT-TTTCTGT
1 TTCTTTC-TTTTCTGTTTCTGT
54767 TTCTTTCTTTTCTGTTTCT
1 TTCTTTCTTTTCTGTTTCT
54786 TTGTATCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.00, C:0.20, G:0.05, T:0.75
Consensus pattern (21 bp):
TTCTTTCTTTTCTGTTTCTGT
Found at i:55290 original size:12 final size:11
Alignment explanation
Indices: 55273--55308 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
55263 GGTCTGTAAT
55273 TATTTATTTATA
1 TATTTATTTA-A
55285 TATTTATTTAA
1 TATTTATTTAA
*
55296 TATGTATTTAA
1 TATTTATTTAA
55307 TA
1 TA
55309 ATAATAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (11 bp):
TATTTATTTAA
Found at i:55312 original size:3 final size:3
Alignment explanation
Indices: 55304--55365 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
55294 AATATGTATT
*
55304 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
55352 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
55366 TGGATAAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:55928 original size:113 final size:112
Alignment explanation
Indices: 55685--56237 Score: 849
Period size: 113 Copynumber: 4.9 Consensus size: 112
55675 AGAGTCATTC
* * * *
55685 AAAAGGTTGAATAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
55750 TATGAACTTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
* *
55797 ATAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCCTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
55862 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
66 TATGAAC-TTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
55910 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
55975 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTTATGAATTCAGGT
66 TATGAAC-TTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
* * *
56023 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTTAAATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* ***
56088 TATGAACCTTCTCTGGCAAAA-ATAATCCATCAAGTGATGAATTCAAAC
66 TATGAA-CTTCTCTGG-AAAAGATGATCCATCAAGTGATGAATTCAGGT
* * *
56136 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
56201 TATGAACTTCTCTGG-AAAGCTGCTCCATCAAGTGATG
66 TATGAACTTCTCTGGAAAAGATGATCCATCAAGTGATG
56238 GATTTGAATC
Statistics
Matches: 406, Mismatches: 31, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
110 3 0.01
111 15 0.04
112 75 0.18
113 308 0.76
114 5 0.01
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (112 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
Found at i:57072 original size:83 final size:83
Alignment explanation
Indices: 56933--57657 Score: 1283
Period size: 83 Copynumber: 8.7 Consensus size: 83
56923 GTTCTTACCA
* * * *
56933 AACCAGATCATATAACTCAAAGAACAATTCCAGAAGATGCTATTGGTAAATTCATCTTCTAAACT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
*
56998 CAATGATTGGTTTTGTCC
66 CAATGATTGGTTCTGTCC
*
57016 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
*
57081 CAATGATTGGTTTTGTCC
66 CAATGATTGGTTCTGTCC
57099 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
57164 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
57182 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
57247 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
*
57265 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATTGGCAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
*
57330 CAATGATCGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
57348 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
57413 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
*
57431 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATTGGCAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
57496 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
* * * *
57514 AACTAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGTACATCCATCTTCTAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCTAAAT
57578 TCAATGATTGGTTCTGTCC
65 TCAATGATTGGTTCTGTCC
*
57597 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCTTCTA
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCTA
57658 GTTAATGTTT
Statistics
Matches: 623, Mismatches: 18, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
82 2 0.00
83 621 1.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.29
Consensus pattern (83 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
CAATGATTGGTTCTGTCC
Found at i:58795 original size:1 final size:1
Alignment explanation
Indices: 58789--58848 Score: 66
Period size: 1 Copynumber: 60.0 Consensus size: 1
58779 TTGACCCTCC
* * * * * *
58789 TTTTTTTTTCTTTCTTTTTTCTTTTTTTTTTTTCTTTTTTTTTTCTTTTTTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
58849 CTTCCTTTTC
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (1 bp):
T
Found at i:58808 original size:11 final size:11
Alignment explanation
Indices: 58788--58848 Score: 83
Period size: 11 Copynumber: 5.8 Consensus size: 11
58778 CTTGACCCTC
58788 CTTT-TTTTTT
1 CTTTCTTTTTT
58798 CTTTCTTTTTT
1 CTTTCTTTTTT
58809 CTTT-TTTTTT
1 CTTTCTTTTTT
58819 -TTTCTTTTTT
1 CTTTCTTTTTT
*
58829 TTTTCTTTTTT
1 CTTTCTTTTTT
*
58840 TTTTCTTTT
1 CTTTCTTTT
58849 CTTCCTTTTC
Statistics
Matches: 48, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
9 3 0.06
10 16 0.33
11 29 0.60
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (11 bp):
CTTTCTTTTTT
Found at i:58821 original size:24 final size:24
Alignment explanation
Indices: 58789--58860 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
58779 TTGACCCTCC
58789 TTTTTTTTTCTTTCTTTTTTCTTT
1 TTTTTTTTTCTTTCTTTTTTCTTT
*
58813 TTTTTTTTTCTTTTTTTTTTCTTT
1 TTTTTTTTTCTTTCTTTTTTCTTT
*
58837 TTTTTTTCT-TTTCTTCCTTTTCTT
1 TTTTTTTTTCTTTCTT--TTTTCTT
58861 CAAGCATAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.12
24 31 0.72
25 7 0.16
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (24 bp):
TTTTTTTTTCTTTCTTTTTTCTTT
Found at i:62408 original size:17 final size:17
Alignment explanation
Indices: 62375--62415 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
62365 TAAATTTATG
*
62375 AAAT-AAATAAATGTAAA
1 AAATAAAATAAATAT-AA
62392 AAATAAAATAAA-ATAA
1 AAATAAAATAAATATAA
62408 AAATAAAA
1 AAATAAAA
62416 AGAATGATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 10 0.45
17 5 0.23
18 7 0.32
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (17 bp):
AAATAAAATAAATATAA
Found at i:71123 original size:15 final size:15
Alignment explanation
Indices: 71105--71155 Score: 86
Period size: 15 Copynumber: 3.4 Consensus size: 15
71095 TAAGTTTCTC
71105 TTCTTTCTTTTTCT-T
1 TTCTTTC-TTTTCTGT
71120 TTCTTTCTTTTCTGT
1 TTCTTTCTTTTCTGT
71135 TTCTTTCTTTTCTGT
1 TTCTTTCTTTTCTGT
71150 TTCTTT
1 TTCTTT
71156 GTATCTCTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.17
15 29 0.83
ACGTcount: A:0.00, C:0.20, G:0.04, T:0.76
Consensus pattern (15 bp):
TTCTTTCTTTTCTGT
Found at i:71124 original size:11 final size:11
Alignment explanation
Indices: 71108--71155 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 11
71098 GTTTCTCTTC
71108 TTTCTTTTTCT
1 TTTCTTTTTCT
71119 TTTC--TTTCT
1 TTTCTTTTTCT
*
71128 TTTCTGTTTC-
1 TTTCTTTTTCT
71138 TTTC-TTTTCT
1 TTTCTTTTTCT
71148 GTTTCTTT
1 -TTTCTTT
71156 GTATCTCTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
9 13 0.42
10 4 0.13
11 12 0.39
12 2 0.06
ACGTcount: A:0.00, C:0.19, G:0.04, T:0.77
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:71126 original size:24 final size:24
Alignment explanation
Indices: 71099--71147 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
71089 TGACAGTAAG
*
71099 TTTCTCTTCT-TTCTTTTTCTTTTC
1 TTTCTCTTCTGTT-TCTTTCTTTTC
*
71123 TTTCTTTTCTGTTTCTTTCTTTTC
1 TTTCTCTTCTGTTTCTTTCTTTTC
71147 T
1 T
71148 GTTTCTTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (24 bp):
TTTCTCTTCTGTTTCTTTCTTTTC
Found at i:71131 original size:20 final size:19
Alignment explanation
Indices: 71099--71155 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 19
71089 TGACAGTAAG
71099 TTTCTCTTC-TTTCTTTTTC
1 TTTCT-TTCTTTTCTTTTTC
*
71118 TTTTCTTTCTTTTCTGTTTC
1 -TTTCTTTCTTTTCTTTTTC
71138 TTTCTTTTCTGTTTCTTT
1 TTTC-TTTCT-TTTCTTT
71156 GTATCTCTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 7 0.22
20 19 0.59
21 6 0.19
ACGTcount: A:0.00, C:0.21, G:0.04, T:0.75
Consensus pattern (19 bp):
TTTCTTTCTTTTCTTTTTC
Found at i:71658 original size:12 final size:11
Alignment explanation
Indices: 71641--71676 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
71631 GGTCTGTAAT
71641 TATTTATTTATA
1 TATTTATTTA-A
71653 TATTTATTTAA
1 TATTTATTTAA
*
71664 TATGTATTTAA
1 TATTTATTTAA
71675 TA
1 TA
71677 ATAATAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (11 bp):
TATTTATTTAA
Found at i:71680 original size:3 final size:3
Alignment explanation
Indices: 71672--71742 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
71662 AATATGTATT
71672 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
71720 TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
71743 TGGATAAAAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:74379 original size:35 final size:35
Alignment explanation
Indices: 74333--74497 Score: 215
Period size: 35 Copynumber: 4.7 Consensus size: 35
74323 ATATGAACAA
* *
74333 TTGAATCGAAAGTGCTTATGCTTCCTCCCATTCAC
1 TTGAATCGAAAGTGCTGATGCTTCCTTCCATTCAC
** * * *
74368 TTGAATCGAAAGTGCCAATGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTGCTGATGCTTCCTTCCATTC-AC
*
74404 TTGAATCGAAAGTGCTGATGCTTCCTTCCGTTCAC
1 TTGAATCGAAAGTGCTGATGCTTCCTTCCATTCAC
* *
74439 TTGAATCAAAAGTGCTGATGCTTCATTCCATTCAC
1 TTGAATCGAAAGTGCTGATGCTTCCTTCCATTCAC
74474 TTGAATCGAAAGTG-TCGATGCTTC
1 TTGAATCGAAAGTGCT-GATGCTTC
74498 TTTTCGTTCT
Statistics
Matches: 114, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
34 1 0.01
35 82 0.72
36 31 0.27
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (35 bp):
TTGAATCGAAAGTGCTGATGCTTCCTTCCATTCAC
Found at i:74451 original size:71 final size:70
Alignment explanation
Indices: 74333--74506 Score: 215
Period size: 71 Copynumber: 2.5 Consensus size: 70
74323 ATATGAACAA
* * * * * * *
74333 TTGAATCGAAAGTGCTTATGCTTCCTCCCATTCACTTGAATCGAAAGTGCCAATGCTTCCTTTCG
1 TTGAATCGAAAGTGCTGATGCTTCCTTCCGTTCACTTGAATCAAAAGTGCCAATGCTTCATTCCA
*
74398 TTCTTC
66 TTC-AC
**
74404 TTGAATCGAAAGTGCTGATGCTTCCTTCCGTTCACTTGAATCAAAAGTGCTGATGCTTCATTCCA
1 TTGAATCGAAAGTGCTGATGCTTCCTTCCGTTCACTTGAATCAAAAGTGCCAATGCTTCATTCCA
74469 TTCAC
66 TTCAC
* *
74474 TTGAATCGAAAGTG-TCGATGCTTCTTTTCGTTC
1 TTGAATCGAAAGTGCT-GATGCTTCCTTCCGTTC
74507 TTATTATTCA
Statistics
Matches: 90, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
69 1 0.01
70 30 0.33
71 59 0.66
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (70 bp):
TTGAATCGAAAGTGCTGATGCTTCCTTCCGTTCACTTGAATCAAAAGTGCCAATGCTTCATTCCA
TTCAC
Found at i:77992 original size:19 final size:19
Alignment explanation
Indices: 77965--78007 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
77955 CCCAAACCGT
*
77965 TTTGACACGACCTGTTGAC
1 TTTGGCACGACCTGTTGAC
77984 TTTGGCACGACCTGTTGAC
1 TTTGGCACGACCTGTTGAC
78003 TTTGG
1 TTTGG
78008 TAGAGTTGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.16, C:0.23, G:0.26, T:0.35
Consensus pattern (19 bp):
TTTGGCACGACCTGTTGAC
Found at i:78605 original size:18 final size:18
Alignment explanation
Indices: 78582--78618 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
78572 TTTACTGGAT
78582 AATGGTTTATGGACTATG
1 AATGGTTTATGGACTATG
78600 AATGGTTTATGGACTATG
1 AATGGTTTATGGACTATG
78618 A
1 A
78619 CTGCATGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.05, G:0.27, T:0.38
Consensus pattern (18 bp):
AATGGTTTATGGACTATG
Found at i:78834 original size:31 final size:31
Alignment explanation
Indices: 78799--78883 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
78789 CTAAGGCGAC
* *
78799 TCTTGGGTAGGCTCTATGACCCTGAGATCTT
1 TCTTGGGTAGGCTCTATGACCCCGAGAACTT
* ** *
78830 TCTTGGGTAGGCCCCGTGGCCCCGAGAACTT
1 TCTTGGGTAGGCTCTATGACCCCGAGAACTT
*
78861 TTTTGGGTAGGCTCT-TAGACCCC
1 TCTTGGGTAGGCTCTAT-GACCCC
78884 AAGATGTTCC
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
30 1 0.02
31 42 0.98
ACGTcount: A:0.14, C:0.27, G:0.28, T:0.31
Consensus pattern (31 bp):
TCTTGGGTAGGCTCTATGACCCCGAGAACTT
Found at i:97050 original size:13 final size:13
Alignment explanation
Indices: 97031--97112 Score: 80
Period size: 13 Copynumber: 6.3 Consensus size: 13
97021 AACCCGACCC
97031 GACCCGACCCGTT
1 GACCCGACCCGTT
*
97044 TACCCGACCCGTT
1 GACCCGACCCGTT
* * *
97057 TACCTGACCAGTT
1 GACCCGACCCGTT
97070 GACCCGACCC---
1 GACCCGACCCGTT
97080 GACCCGACCCGTT
1 GACCCGACCCGTT
97093 GACCCGTTGACCCGTT
1 GACCC---GACCCGTT
97109 GACC
1 GACC
97113 GTTGACCCAC
Statistics
Matches: 57, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
10 10 0.18
13 35 0.61
16 12 0.21
ACGTcount: A:0.17, C:0.44, G:0.21, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:97116 original size:7 final size:8
Alignment explanation
Indices: 97085--97133 Score: 66
Period size: 8 Copynumber: 6.1 Consensus size: 8
97075 GACCCGACCC
97085 GACCCGTT
1 GACCCGTT
97093 GACCCGTT
1 GACCCGTT
97101 GACCCGTT
1 GACCCGTT
97109 GA-CCGTT
1 GACCCGTT
97116 GACCCACGTT
1 GA-CC-CGTT
97126 GA-CCGTT
1 GACCCGTT
97133 G
1 G
97134 TTGACCAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
7 12 0.32
8 19 0.50
9 1 0.03
10 6 0.16
ACGTcount: A:0.14, C:0.35, G:0.27, T:0.24
Consensus pattern (8 bp):
GACCCGTT
Found at i:100010 original size:61 final size:63
Alignment explanation
Indices: 99945--100065 Score: 149
Period size: 63 Copynumber: 2.0 Consensus size: 63
99935 TAATGTGACA
* ** * *
99945 CTTAGGTAGGCTCTGCGGCCCTGAGATC-AT-TCGGGTAGGCCCTGC-GGCCCTAAGATGTGTT
1 CTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGTT
* *
100006 CTTAGGTAGGCCCCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 CTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
100066 TCCCTTAGGT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
61 23 0.46
62 3 0.06
63 24 0.48
ACGTcount: A:0.17, C:0.28, G:0.30, T:0.25
Consensus pattern (63 bp):
CTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGTT
Found at i:104123 original size:23 final size:23
Alignment explanation
Indices: 104097--104146 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
104087 TAAAAGGGGT
104097 AATCCTTCAATGAAATACATGGA
1 AATCCTTCAATGAAATACATGGA
104120 AATCCTTCAATGAAATACATGGA
1 AATCCTTCAATGAAATACATGGA
104143 AATC
1 AATC
104147 ATTTCCCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (23 bp):
AATCCTTCAATGAAATACATGGA
Done.