Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007754.1 Hibiscus syriacus cultivar Beakdansim tig00110020_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: 3698414
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 15
Found at i:3575557 original size:130 final size:132
Alignment explanation
Indices: 3575338--3575604 Score: 412
Period size: 130 Copynumber: 2.0 Consensus size: 132
3575328 TTCAAAAACA
* *
3575338 TCATATCGGATGGAGGAAAATGGCTTCCGCATTTCTATATTGCATGACTAAGCCCTACTAAGGAG
1 TCATATCGGATGGAGGAAAATGACTTCCACATTTCTATATTGCATGACTAAGCCCTACTAAGGAG
* * * *
3575403 TACTCTTTTAAAGATGTAAACAAG-A-TCTTTTTCTATGTTCTTACTTGCATAAAAATAGCCATA
66 TACGCTTTTAAAGATGTAAACAAGAACTATTTTTCAATGTTCTTACTTGCATAAAAATAACCATA
3575466 TT
131 TT
* * *
3575468 TCATATCGGATGGAGGAAAATGACTTCCATATTTCTATATTGCATGACTAAGCCCTACTAGGGTG
1 TCATATCGGATGGAGGAAAATGACTTCCACATTTCTATATTGCATGACTAAGCCCTACTAAGGAG
* *
3575533 TACGCTTTTAAAGATGTTAGCAAGAACTTATTTTTCAATGTTCTTACTTGCATAAAAATAACCAT
66 TACGCTTTTAAAGATGTAAACAAGAAC-TATTTTTCAATGTTCTTACTTGCATAAAAATAACCAT
3575598 ATT
130 ATT
3575601 TCAT
1 TCAT
3575605 GGAACAAACT
Statistics
Matches: 123, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
130 81 0.66
131 1 0.01
133 41 0.33
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (132 bp):
TCATATCGGATGGAGGAAAATGACTTCCACATTTCTATATTGCATGACTAAGCCCTACTAAGGAG
TACGCTTTTAAAGATGTAAACAAGAACTATTTTTCAATGTTCTTACTTGCATAAAAATAACCATA
TT
Found at i:3584020 original size:17 final size:15
Alignment explanation
Indices: 3583972--3584007 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
3583962 GTTTTTTCTT
*
3583972 ATTACTTCGTGATTC
1 ATTACTTCATGATTC
3583987 ATTACTTCATGATTC
1 ATTACTTCATGATTC
3584002 ATTACT
1 ATTACT
3584008 CATCATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.47
Consensus pattern (15 bp):
ATTACTTCATGATTC
Found at i:3587329 original size:6 final size:6
Alignment explanation
Indices: 3587312--3587349 Score: 67
Period size: 6 Copynumber: 6.2 Consensus size: 6
3587302 GGAAAACTTT
3587312 CTCTCTC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC C
1 CTCTC-C CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC C
3587350 GCAACAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (6 bp):
CTCTCC
Found at i:3594611 original size:19 final size:19
Alignment explanation
Indices: 3594578--3594617 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3594568 TATTTAAGTT
*
3594578 TATACATATTAATTATTAA
1 TATACATATTAATTAATAA
3594597 TATACTATATT-ATTAATAA
1 TATAC-ATATTAATTAATAA
3594616 TA
1 TA
3594618 GATAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
TATACATATTAATTAATAA
Found at i:3604766 original size:21 final size:22
Alignment explanation
Indices: 3604741--3604782 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
3604731 TATTATAAGT
**
3604741 ATATTTATGAATAT-ATAAAAA
1 ATATTTAACAATATAATAAAAA
3604762 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
3604783 TAAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
ATATTTAACAATATAATAAAAA
Found at i:3605425 original size:10 final size:10
Alignment explanation
Indices: 3605410--3605435 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3605400 GCGAGTTCTG
3605410 CCGCCGACCA
1 CCGCCGACCA
3605420 CCGCCGACCA
1 CCGCCGACCA
3605430 CCGCCG
1 CCGCCG
3605436 CCGGTGGTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.15, C:0.62, G:0.23, T:0.00
Consensus pattern (10 bp):
CCGCCGACCA
Found at i:3606248 original size:3 final size:3
Alignment explanation
Indices: 3606240--3606350 Score: 150
Period size: 3 Copynumber: 36.7 Consensus size: 3
3606230 TAATATAAAT
*
3606240 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
** * **
3606286 TAA TAA TAA TAA GGA TAA TAA TAA TAT TAA TAA TAA TAA GGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
3606334 TAA TAT TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
3606351 TGGATAAAAA
Statistics
Matches: 93, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
3 90 0.97
4 3 0.03
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3606800 original size:113 final size:113
Alignment explanation
Indices: 3606602--3607262 Score: 1047
Period size: 113 Copynumber: 5.8 Consensus size: 113
3606592 TCTTGATGAG
3606602 TTCTTCTCATTATGAACTT-TCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-C
1 TTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTC
* * * *
3606665 TGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
64 TGGAAAAGTTGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAA
*
3606715 TTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * *
3606780 GAAAAGATGATTCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGTTGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAA
* *
3606828 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * ** * *
3606893 GCAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAG
66 GAAAAGTTGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAA
*
3606941 TTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
3607006 GAAAAGCTGATCCATCAAATGACGGATTCAAGTAAAAGGTTGAACAAA
66 GAAAAGTTGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAA
3607054 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
3607119 GAAAAGTTAATCCATCAAATGACGGATTCAAGTAAAAGGTTGAACAAA
66 GAAAAGTTGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAA
*
3607167 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
3607232 GAAAAGCTGTTCCATCAAATGATGGATTCAA
66 GAAAAGTTGATCCATCAAATGATGGATTCAA
3607263 ATCTTTGCTA
Statistics
Matches: 501, Mismatches: 45, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
112 1 0.00
113 499 1.00
114 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGTTGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAA
Found at i:3608022 original size:83 final size:82
Alignment explanation
Indices: 3607876--3608056 Score: 290
Period size: 83 Copynumber: 2.2 Consensus size: 82
3607866 TTTACTATGA
* *
3607876 GCAAATTCATCTTCCAAATTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCCAAATTCAATGATTGTTCTATACAACCAGATCAGATAACTCAAAGAACACT
3607941 TCCAGAAGATGCTATTG
66 TCCAGAAGATGCTATTG
* * * *
3607958 GCAAATTCATCTTCCAAATTCAATGCTTGGTTCTATATAATCAGGTCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAATTCAATGATT-GTTCTATACAACCAGATCAGATAACTCAAAGAACAC
3608023 TTCCAGAAGATGCTATTG
65 TTCCAGAAGATGCTATTG
*
3608041 GTAAATTCATCTTCCA
1 GCAAATTCATCTTCCA
3608057 TTTAATGTTT
Statistics
Matches: 91, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
82 27 0.30
83 64 0.70
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (82 bp):
GCAAATTCATCTTCCAAATTCAATGATTGTTCTATACAACCAGATCAGATAACTCAAAGAACACT
TCCAGAAGATGCTATTG
Found at i:3609206 original size:19 final size:18
Alignment explanation
Indices: 3609179--3609257 Score: 69
Period size: 17 Copynumber: 4.5 Consensus size: 18
3609169 CTTGACCCCC
*
3609179 TTTCTTTTTCTTCTCTTTT
1 TTTCATTTTCTT-TCTTTT
*
3609198 TTTCATTTTCTAT-TTTT
1 TTTCATTTTCTTTCTTTT
3609215 TTTCTATTTT-TTTCTTTT
1 TTTC-ATTTTCTTTCTTTT
*
3609233 CTTTC-TTTTCTTT-TTCT
1 -TTTCATTTTCTTTCTTTT
3609250 TTTC-TTTT
1 TTTCATTTT
3609258 TTCTTCAAGC
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
16 8 0.15
17 17 0.33
18 13 0.25
19 14 0.27
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTCATTTTCTTTCTTTT
Found at i:3609217 original size:30 final size:28
Alignment explanation
Indices: 3609179--3609259 Score: 92
Period size: 30 Copynumber: 2.8 Consensus size: 28
3609169 CTTGACCCCC
*
3609179 TTTCTTTTTCTTCTCTTTTTTTCATTTTCT
1 TTTCTTTTTCTTTTCTTTTTTTC--TTTCT
*
3609209 ATTT-TTTTTCTATTTTTTTCTTTTCTTTCT
1 -TTTCTTTTTCT-TTTCTTT-TTTTCTTTCT
3609239 TTTCTTTTTCTTTTCTTTTTT
1 TTTCTTTTTCTTTTCTTTTTT
3609260 CTTCAAGCAT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
28 3 0.07
29 9 0.20
30 19 0.43
31 8 0.18
32 5 0.11
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (28 bp):
TTTCTTTTTCTTTTCTTTTTTTCTTTCT
Found at i:3609219 original size:27 final size:26
Alignment explanation
Indices: 3609183--3609257 Score: 82
Period size: 27 Copynumber: 2.9 Consensus size: 26
3609173 ACCCCCTTTC
*
3609183 TTTTTCTTCTCTTTTTTTCATTTTCTA
1 TTTTTTTTCTCTTTTTTTC-TTTTCTA
*
3609210 TTTTTTTTCTATTTTTTTCTTTTC--
1 TTTTTTTTCTCTTTTTTTCTTTTCTA
* *
3609234 TTTCTTTTCTTTTTCTTTTCTTTT
1 TTTTTTTTCTCTTT-TTTTCTTTT
3609258 TTCTTCAAGC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
24 12 0.28
25 9 0.21
26 5 0.12
27 17 0.40
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (26 bp):
TTTTTTTTCTCTTTTTTTCTTTTCTA
Found at i:3609234 original size:5 final size:5
Alignment explanation
Indices: 3609179--3609257 Score: 67
Period size: 5 Copynumber: 15.6 Consensus size: 5
3609169 CTTGACCCCC
* *
3609179 TTTCT TTT-T CTTCT CTTT-T TTTCAT TTTCT ATTTTT TTTCT ATTT-T
1 TTTCT TTTCT TTTCT -TTTCT TTTC-T TTTCT -TTTCT TTTCT -TTTCT
3609225 TTTCT TTTC- TTTCT TTTCTT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTC-T TTTCT TTTCT TTT
3609258 TTCTTCAAGC
Statistics
Matches: 61, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
4 13 0.21
5 29 0.48
6 19 0.31
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:3619918 original size:17 final size:17
Alignment explanation
Indices: 3619878--3619919 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
3619868 ATACTTGCAA
*
3619878 ATAAAACATATAAATATT
1 ATAAAA-ATATAAATATC
3619896 ATAAAAATAATAAATA-C
1 ATAAAAAT-ATAAATATC
3619913 ATAAAAA
1 ATAAAAA
3619920 ATTTGAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (17 bp):
ATAAAAATATAAATATC
Found at i:3620646 original size:21 final size:22
Alignment explanation
Indices: 3620621--3620662 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
3620611 TATTATAAGT
**
3620621 ATATTTATGAATAT-ATAAAAA
1 ATATTTAACAATATAATAAAAA
3620642 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
3620663 TAAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
ATATTTAACAATATAATAAAAA
Found at i:3622122 original size:3 final size:3
Alignment explanation
Indices: 3622114--3622262 Score: 199
Period size: 3 Copynumber: 49.7 Consensus size: 3
3622104 TAATATAAAT
*
3622114 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* ** * **
3622162 TAA TAT TAA TAA TAA TAA GGA TAA TAA TAA TAT TAA TAA TAA TAA GGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* ** *
3622210 TAA TAA TAA TAT TAA TAA TAA TAA GGA TAA TAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3622258 TAA TA
1 TAA TA
3622263 TGGATAAAAA
Statistics
Matches: 124, Mismatches: 22, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 124 1.00
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3622269 original size:27 final size:27
Alignment explanation
Indices: 3622104--3622260 Score: 264
Period size: 27 Copynumber: 5.9 Consensus size: 27
3622094 TTAATATATT
**
3622104 TAAT-ATAA-ATTAATAATAATAATAA
1 TAATAATAATATTAATAATAATAAGGA
* *
3622129 TAATAATAATAATAATAATAATAATGA
1 TAATAATAATATTAATAATAATAAGGA
3622156 TAATAATAATATTAATAATAATAAGGA
1 TAATAATAATATTAATAATAATAAGGA
3622183 TAATAATAATATTAATAATAATAAGGA
1 TAATAATAATATTAATAATAATAAGGA
3622210 TAATAATAATATTAATAATAATAAGGA
1 TAATAATAATATTAATAATAATAAGGA
3622237 TAATAATAATATTAATAATAATAA
1 TAATAATAATATTAATAATAATAA
3622261 TATGGATAAA
Statistics
Matches: 126, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
25 4 0.03
26 4 0.03
27 118 0.94
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.34
Consensus pattern (27 bp):
TAATAATAATATTAATAATAATAAGGA
Found at i:3624286 original size:32 final size:32
Alignment explanation
Indices: 3624246--3624445 Score: 233
Period size: 32 Copynumber: 6.2 Consensus size: 32
3624236 TAAAATGTTA
3624246 TATATAATTGATCAAAGCATATGGAAATATTT
1 TATATAATTGATCAAAGCATATGGAAATATTT
*
3624278 TATATAATTGATCAAAGCA-AGTGGAAATATTC
1 TATATAATTGATCAAAGCATA-TGGAAATATTT
* *
3624310 TATATAATTAATCAAAGCA-AGTGGAAATGTTT
1 TATATAATTGATCAAAGCATA-TGGAAATATTT
* * *
3624342 TATATAATTGGTCAAAGTATGTGGAAATATTT
1 TATATAATTGATCAAAGCATATGGAAATATTT
* * * * *
3624374 TATATAATTAATCAAAACATATGGAGATAATA
1 TATATAATTGATCAAAGCATATGGAAATATTT
*
3624406 TATATAGTTGATCAAAGCATATGAAGGAAATATTT
1 TATATAATTGATCAAAGCATAT---GGAAATATTT
3624441 TATAT
1 TATAT
3624446 TCAAGGAGCA
Statistics
Matches: 140, Mismatches: 23, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
31 1 0.01
32 127 0.91
35 12 0.09
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.35
Consensus pattern (32 bp):
TATATAATTGATCAAAGCATATGGAAATATTT
Found at i:3624410 original size:96 final size:96
Alignment explanation
Indices: 3624238--3624424 Score: 259
Period size: 96 Copynumber: 1.9 Consensus size: 96
3624228 ACTTTTAATA
* *
3624238 AAATGTTATATATAATTGATCAAAGCATATGGAAATATTTTATATAATTGATCAAAGCAAGTGGA
1 AAATGTTATATATAATTGATCAAAGCATATGGAAATATTTTATATAATTAATCAAAACAAGTGGA
* *
3624303 AATATTCTATATAATTAATCAAAGCAAGTGG
66 AATAATATATATAATTAATCAAAGCAAGTGG
* * * *
3624334 AAATGTTTTATATAATTGGTCAAAGTATGTGGAAATATTTTATATAATTAATCAAAACATA-TGG
1 AAATGTTATATATAATTGATCAAAGCATATGGAAATATTTTATATAATTAATCAAAACA-AGTGG
* * *
3624398 AGATAATATATATAGTTGATCAAAGCA
65 AAATAATATATATAATTAATCAAAGCA
3624425 TATGAAGGAA
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
96 78 0.99
97 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.35
Consensus pattern (96 bp):
AAATGTTATATATAATTGATCAAAGCATATGGAAATATTTTATATAATTAATCAAAACAAGTGGA
AATAATATATATAATTAATCAAAGCAAGTGG
Found at i:3624956 original size:16 final size:16
Alignment explanation
Indices: 3624935--3624965 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3624925 TAAATCAAAT
*
3624935 AATATTTTTTTTAAAA
1 AATATTATTTTTAAAA
3624951 AATATTATTTTTAAA
1 AATATTATTTTTAAA
3624966 TAAAAGATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AATATTATTTTTAAAA
Found at i:3630818 original size:25 final size:25
Alignment explanation
Indices: 3630790--3630867 Score: 156
Period size: 25 Copynumber: 3.1 Consensus size: 25
3630780 CTTTTTTATA
3630790 TGATCATATGTATGAAATTACCATT
1 TGATCATATGTATGAAATTACCATT
3630815 TGATCATATGTATGAAATTACCATT
1 TGATCATATGTATGAAATTACCATT
3630840 TGATCATATGTATGAAATTACCATT
1 TGATCATATGTATGAAATTACCATT
3630865 TGA
1 TGA
3630868 CACGATCCTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.40
Consensus pattern (25 bp):
TGATCATATGTATGAAATTACCATT
Found at i:3633535 original size:16 final size:16
Alignment explanation
Indices: 3633514--3633554 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
3633504 AAATGATCCG
* *
3633514 GACTCGGACTTAATAT
1 GACTCGAACTTAAAAT
3633530 GACTCGAACTTAAAAT
1 GACTCGAACTTAAAAT
*
3633546 GATTCGAAC
1 GACTCGAAC
3633555 AAGTACTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.27
Consensus pattern (16 bp):
GACTCGAACTTAAAAT
Found at i:3666398 original size:93 final size:93
Alignment explanation
Indices: 3666239--3666427 Score: 288
Period size: 93 Copynumber: 2.0 Consensus size: 93
3666229 TTTTAAAAGA
* * * * *
3666239 TACATATGCATCTATTAAACATTAGTTTAGTTGATAGAGAATATGGAAAGTTTAAGTATTGTATA
1 TACATATGCATCTACTAAACATTAGTTCAATTCATAGAGAATAAGGAAAGTTTAAGTATTGTATA
*
3666304 AATATATAGATATAAGTTATTATTTTTG
66 AATATATACATATAAGTTATTATTTTTG
* * *
3666332 TACATATGCATCTACTGAATATTAGTTCAATTCATAGGGAATAAGGAAAGTTTAAGTATTGTATA
1 TACATATGCATCTACTAAACATTAGTTCAATTCATAGAGAATAAGGAAAGTTTAAGTATTGTATA
*
3666397 AATATATACATATAAGTTATTCTTTTTG
66 AATATATACATATAAGTTATTATTTTTG
3666425 TAC
1 TAC
3666428 TGACAGTAAA
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 86 1.00
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (93 bp):
TACATATGCATCTACTAAACATTAGTTCAATTCATAGAGAATAAGGAAAGTTTAAGTATTGTATA
AATATATACATATAAGTTATTATTTTTG
Found at i:3666475 original size:19 final size:19
Alignment explanation
Indices: 3666451--3666507 Score: 96
Period size: 19 Copynumber: 2.9 Consensus size: 19
3666441 ATATTCCTCA
3666451 CGTTTGTCTATTTGAATGT
1 CGTTTGTCTATTTGAATGT
3666470 CGTTTGTCTATTTGAATGT
1 CGTTTGTCTATTTGAATGT
*
3666489 CATTTGTCATATTTGAATG
1 CGTTTGTC-TATTTGAATG
3666508 ATTCTAAACC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
19 26 0.72
20 10 0.28
ACGTcount: A:0.19, C:0.11, G:0.19, T:0.51
Consensus pattern (19 bp):
CGTTTGTCTATTTGAATGT
Found at i:3666533 original size:20 final size:19
Alignment explanation
Indices: 3666508--3666547 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
3666498 TATTTGAATG
*
3666508 ATTCTAAACCTTAAATCATA
1 ATTCTAAACCCTAAAT-ATA
3666528 ATTCTAAACCCTAAATATA
1 ATTCTAAACCCTAAATATA
3666547 A
1 A
3666548 AAAAATCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTCTAAACCCTAAATATA
Found at i:3668455 original size:20 final size:20
Alignment explanation
Indices: 3668430--3668468 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3668420 TACTTTAAAA
3668430 TTTAATTTAATTCTATATTG
1 TTTAATTTAATTCTATATTG
* *
3668450 TTTAATTTGATTTTATATT
1 TTTAATTTAATTCTATATT
3668469 TTATTATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (20 bp):
TTTAATTTAATTCTATATTG
Found at i:3677355 original size:25 final size:25
Alignment explanation
Indices: 3677321--3677374 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
3677311 GAAACGAGAG
*
3677321 TATTCTAATAATATAATGTATAATT
1 TATTCTAATAATATAATATATAATT
* * *
3677346 TATTGTAATAATTTAATATTTAATT
1 TATTCTAATAATATAATATATAATT
3677371 TATT
1 TATT
3677375 AATCGATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.54
Consensus pattern (25 bp):
TATTCTAATAATATAATATATAATT
Found at i:3684246 original size:20 final size:20
Alignment explanation
Indices: 3684221--3684263 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
3684211 CTTCAATCAT
3684221 GCCCTATAAGGATCCACCAC
1 GCCCTATAAGGATCCACCAC
3684241 GCCCTATAAGGATCCACCAC
1 GCCCTATAAGGATCCACCAC
3684261 GCC
1 GCC
3684264 AATAATATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.42, G:0.16, T:0.14
Consensus pattern (20 bp):
GCCCTATAAGGATCCACCAC
Found at i:3695965 original size:114 final size:114
Alignment explanation
Indices: 3695765--3695995 Score: 399
Period size: 114 Copynumber: 2.0 Consensus size: 114
3695755 ACATTACGGT
* *
3695765 TCTCAATCTCGCCAACACGGTTGCACTTTCGAACGATCGGAAGCCGCCTTCGGTAAACCAGTCCG
1 TCTCAATCTCGCCAACACCGCTGCACTTTCGAACGATCGGAAGCCGCCTTCGGTAAACCAGTCCG
*
3695830 ACGTTCTCGCATTGCAGCGAAAGCTGGCCGGTATGTCAAGAGGTGCAGG
66 ACGTTCTCACATTGCAGCGAAAGCTGGCCGGTATGTCAAGAGGTGCAGG
* * *
3695879 TCTCAGTCTCGCCAACACCGCTGCGCTTTCGAACTATCGGAAGCCGCCTTCGGTAAACCAGTCCG
1 TCTCAATCTCGCCAACACCGCTGCACTTTCGAACGATCGGAAGCCGCCTTCGGTAAACCAGTCCG
*
3695944 ACGTTCTCACATTGCAGCGAAAGCTGGCTGGTATGTCAAGAGGTGCAGG
66 ACGTTCTCACATTGCAGCGAAAGCTGGCCGGTATGTCAAGAGGTGCAGG
3695993 TCT
1 TCT
3695996 TAATTGGAAT
Statistics
Matches: 110, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 110 1.00
ACGTcount: A:0.22, C:0.29, G:0.26, T:0.22
Consensus pattern (114 bp):
TCTCAATCTCGCCAACACCGCTGCACTTTCGAACGATCGGAAGCCGCCTTCGGTAAACCAGTCCG
ACGTTCTCACATTGCAGCGAAAGCTGGCCGGTATGTCAAGAGGTGCAGG
Found at i:3698326 original size:28 final size:28
Alignment explanation
Indices: 3698295--3698355 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
3698285 CAAATACAAG
3698295 ATTTTATGTTAGAAGAATGAAATTATAA
1 ATTTTATGTTAGAAGAATGAAATTATAA
*
3698323 ATTTTATGTTAGATGAATGAAATTATAA
1 ATTTTATGTTAGAAGAATGAAATTATAA
3698351 ATTTT
1 ATTTT
3698356 TTGAAGATAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.44
Consensus pattern (28 bp):
ATTTTATGTTAGAAGAATGAAATTATAA
Done.