Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003827.1 Hibiscus syriacus cultivar Beakdansim tig00008205_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: 71767
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:3563 original size:17 final size:16
Alignment explanation
Indices: 3536--3567 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
3526 TATCTTTTAA
3536 TAAAAATATTAATTAT
1 TAAAAATATTAATTAT
3552 TAAAATATATTAATTA
1 TAAAA-ATATTAATTA
3568 ATAATTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAAAATATTAATTAT
Found at i:3598 original size:29 final size:29
Alignment explanation
Indices: 3530--3599 Score: 70
Period size: 30 Copynumber: 2.4 Consensus size: 29
3520 ATAGAGTATC
* *
3530 TTTTAATAAAAATATTAATTATTAAAATA
1 TTTTAATAATAATATTAATAATTAAAATA
* * *
3559 TATTAATTAATAATTTTAATAA-TATAATA
1 TTTTAA-TAATAATATTAATAATTAAAATA
3588 TTTTTAATAATA
1 -TTTTAATAATA
3600 TACTATTATA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
TTTTAATAATAATATTAATAATTAAAATA
Found at i:3606 original size:17 final size:17
Alignment explanation
Indices: 3562--3606 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
3552 TAAAATATAT
*
3562 TAAT-TAATAATTTTAA
1 TAATATAATATTTTTAA
3578 TAATATAATATTTTTAA
1 TAATATAATATTTTTAA
*
3595 TAATATACTATT
1 TAATATAATATT
3607 ATATTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 4 0.15
17 22 0.85
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
TAATATAATATTTTTAA
Found at i:3607 original size:44 final size:44
Alignment explanation
Indices: 3530--3628 Score: 107
Period size: 44 Copynumber: 2.3 Consensus size: 44
3520 ATAGAGTATC
*
3530 TTTTAATAA-A-AATATTAATTATTAAAATATATTA-ATTAATAA
1 TTTTAATAATATAATATTAATTAATAAAATATATTATATT-ATAA
* * * *
3572 TTTTAATAATATAATATT-TTTAATAATATACTATTATATTTTTA
1 TTTTAATAATATAATATTAATTAATAAAATA-TATTATATTATAA
3616 TTTTAATAATATA
1 TTTTAATAATATA
3629 TAATAAATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
42 9 0.19
43 10 0.21
44 26 0.54
45 3 0.06
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (44 bp):
TTTTAATAATATAATATTAATTAATAAAATATATTATATTATAA
Found at i:3749 original size:14 final size:14
Alignment explanation
Indices: 3727--3759 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
3717 ATTTCCATAA
3727 TATAA-TTTAATAT
1 TATAATTTTAATAT
3740 TATAATTTTAATAT
1 TATAATTTTAATAT
3754 TATAAT
1 TATAAT
3760 AATATTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TATAATTTTAATAT
Found at i:3819 original size:26 final size:25
Alignment explanation
Indices: 3788--3845 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
3778 AAGTAATAAA
*
3788 TATAATTAATAATATAATAAT-ATTTT
1 TATAATAAATAAT-TAA-AATAATTTT
*
3814 TATAATAAATCATTAAAATAATTTT
1 TATAATAAATAATTAAAATAATTTT
*
3839 TAAAATA
1 TATAATA
3846 CTTATTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 3 0.11
25 14 0.50
26 11 0.39
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
TATAATAAATAATTAAAATAATTTT
Found at i:4158 original size:14 final size:14
Alignment explanation
Indices: 4124--4152 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
4114 AGAATGCAAT
4124 TCATTTTATGAAAA
1 TCATTTTATGAAAA
4138 TCATTTT-TGAAAA
1 TCATTTTATGAAAA
4151 TC
1 TC
4153 TGTTTTCTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (14 bp):
TCATTTTATGAAAA
Found at i:6510 original size:58 final size:58
Alignment explanation
Indices: 6434--6597 Score: 181
Period size: 56 Copynumber: 2.8 Consensus size: 58
6424 TTAATAAATT
* * * * *
6434 ATTTTAATATTT-AGATAAACTATGTAAATAATGTCTGGTTTTGATCATCGAACTAGTCA
1 ATTTT-ATATTTGA-ATAAACTATATAAATAATGTTTGATTTTGATCATCGAACCAATCA
* * *
6493 ATTTTATATTTGAATAAA--ATATAAATACTGTTTGATTTTGATAATCGGACCAATCA
1 ATTTTATATTTGAATAAACTATATAAATAATGTTTGATTTTGATCATCGAACCAATCA
* ** *
6549 ATTTTATATTTGGATAAACTATATGGATAATGTTTGATTTTGGTCATCG
1 ATTTTATATTTGAATAAACTATATAAATAATGTTTGATTTTGATCATCG
6598 GAGTTGGACC
Statistics
Matches: 88, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
56 47 0.53
58 35 0.40
59 6 0.07
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.43
Consensus pattern (58 bp):
ATTTTATATTTGAATAAACTATATAAATAATGTTTGATTTTGATCATCGAACCAATCA
Found at i:7105 original size:71 final size:71
Alignment explanation
Indices: 7017--7159 Score: 259
Period size: 71 Copynumber: 2.0 Consensus size: 71
7007 TCAATCACTA
* *
7017 AGGTTTAATGTAAAATTAAGTGTCTAAACTATACTCAAAATTAACTTTAGGTGTCTAAAGAATTT
1 AGGTTTAATGTAAAATTAAGTGTCTAAACTATAATCAAAATTAACTTTAGGTGTCCAAAGAATTT
7082 TTCATT
66 TTCATT
*
7088 AGGTTTAATGTAAAATTAAGTGTCTAAACTATAATCAAGATTAACTTTAGGTGTCCAAAGAATTT
1 AGGTTTAATGTAAAATTAAGTGTCTAAACTATAATCAAAATTAACTTTAGGTGTCCAAAGAATTT
7153 TTCATT
66 TTCATT
7159 A
1 A
7160 AAAAGAGGAG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (71 bp):
AGGTTTAATGTAAAATTAAGTGTCTAAACTATAATCAAAATTAACTTTAGGTGTCCAAAGAATTT
TTCATT
Found at i:7514 original size:24 final size:25
Alignment explanation
Indices: 7483--7553 Score: 99
Period size: 24 Copynumber: 2.9 Consensus size: 25
7473 TGCCATATAG
*
7483 ATTTGTCTCGAATGACCGCGTAG-A
1 ATTTGTCTCGAAAGACCGCGTAGAA
* *
7507 ATTTGTCTCGAAGGACCACGTAGAA
1 ATTTGTCTCGAAAGACCGCGTAGAA
*
7532 ATTTGTCCCGAAAGACCGCGTA
1 ATTTGTCTCGAAAGACCGCGTA
7554 TAACCCTCGA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
24 21 0.51
25 20 0.49
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (25 bp):
ATTTGTCTCGAAAGACCGCGTAGAA
Found at i:7735 original size:15 final size:15
Alignment explanation
Indices: 7696--7756 Score: 70
Period size: 15 Copynumber: 4.1 Consensus size: 15
7686 TATTTTCATG
*
7696 TAGAACATTTTCACG
1 TAGAACATTTTCACA
* *
7711 TAGCATATTTTCACA
1 TAGAACATTTTCACA
*
7726 TAGAACATTTTCATA
1 TAGAACATTTTCACA
*
7741 TA-AACATATTCACA
1 TAGAACATTTTCACA
7755 TA
1 TA
7757 CAAATAAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
14 12 0.32
15 26 0.68
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (15 bp):
TAGAACATTTTCACA
Found at i:9765 original size:3 final size:3
Alignment explanation
Indices: 9759--9846 Score: 105
Period size: 3 Copynumber: 30.7 Consensus size: 3
9749 CATTTGGTTG
*
9759 TAT TAT TAT TAT TAA TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
9805 TAT TA- TAT TAT AAT T-T TAAT TA- TAA TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TA
9847 CAGGCCCAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 12
0.81 0.05 0.13
Matches are distributed among these distances:
2 10 0.14
3 62 0.84
4 2 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:9784 original size:20 final size:20
Alignment explanation
Indices: 9759--9846 Score: 98
Period size: 20 Copynumber: 4.5 Consensus size: 20
9749 CATTTGGTTG
9759 TATTATTATTATTAATATTA
1 TATTATTATTATTAATATTA
*
9779 TATTATTATTATTATTA-T-
1 TATTATTATTATTAATATTA
9797 TATTATT-TTATT-ATATTA
1 TATTATTATTATTAATATTA
9815 TAATT-TTAATTA-TAATATTA
1 T-ATTATT-ATTATTAATATTA
9835 TTATTATTATTA
1 -TATTATTATTA
9847 CAGGCCCAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
16 2 0.03
17 6 0.10
18 10 0.17
19 5 0.09
20 32 0.55
21 3 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTATTATTATTAATATTA
Found at i:11227 original size:3 final size:3
Alignment explanation
Indices: 11219--11245 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
11209 AATATATTTA
11219 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
11246 TAGTCATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:11631 original size:155 final size:160
Alignment explanation
Indices: 11315--11641 Score: 445
Period size: 155 Copynumber: 2.1 Consensus size: 160
11305 AAATCTTATT
11315 TATA-AATTTAATTTTATATAAATTATTTTTATGAAAAATAATCATATTTTAATATTTATTTATT
1 TATATAATTTAATTTTATATAAATTATTTTTATGAAAAATAAT-ATATTTTAATATTTATTTATT
* *
11379 TTTTAATATTAAGAAAATGATTGTCTTAAAGCAACTAGAAGTCCTTTTCTGATATTTTTAAATAA
65 TTTTAATATTAAGAAAATGACTGTCTTAAAGCAACTAGAAGTCCTTTTCTGATATTTCTAAATAA
* * * * *
11444 CTAAATATCTTACTTTTATAAATTATATATA
130 ATAAATATCTTACTTTTAAAAATAAAAAATA
* * *
11475 TAT-TAATTTAA-TTTATTTTAATTATTTTTA-GAGAAAT-AT-T-TTATTAATATTTATTTATT
1 TATATAATTTAATTTTATATAAATTATTTTTATGAAAAATAATATATT-TTAATATTTATTTATT
* *
11534 TTTTAATATTAAGAAAATGACTGTCTTAAAGCAACTAGAAGTCTTTTTCTGATATTTCTAAGTAA
65 TTTTAATATTAAGAAAATGACTGTCTTAAAGCAACTAGAAGTCCTTTTCTGATATTTCTAAATAA
*
11599 ATAAATATTTTA-TTTATAAAAATAAAAAATA
130 ATAAATATCTTACTTT-TAAAAATAAAAAATA
11630 TATATATATTTA
1 TATATA-ATTTA
11642 TAAAAGTTAA
Statistics
Matches: 149, Mismatches: 13, Indels: 13
0.85 0.07 0.07
Matches are distributed among these distances:
154 5 0.03
155 102 0.68
156 2 0.01
157 7 0.05
158 6 0.04
159 17 0.11
160 10 0.07
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.48
Consensus pattern (160 bp):
TATATAATTTAATTTTATATAAATTATTTTTATGAAAAATAATATATTTTAATATTTATTTATTT
TTTAATATTAAGAAAATGACTGTCTTAAAGCAACTAGAAGTCCTTTTCTGATATTTCTAAATAAA
TAAATATCTTACTTTTAAAAATAAAAAATA
Found at i:11678 original size:155 final size:155
Alignment explanation
Indices: 11364--11678 Score: 386
Period size: 155 Copynumber: 2.0 Consensus size: 155
11354 AATCATATTT
*
11364 TAATATTTATTTATTTTTTAATATTAAGAAAATGATTGTCTTAAAGCAACTAGAAGTCCTTTTCT
1 TAATATTTATTTATTTTTTAATATTAAGAAAATGACTGTCTTAAAGCAACTAGAAGTCCTTTTCT
* * * * * * ** **
11429 GATATTTTTAAATAACTAAATATCTTACTTTTATAAATTATATATATATTAATTTAATTTATTTT
66 GATATTTCTAAATAAATAAATATCTTACTTTTAAAAATAAAAAATATATTAATTTAATAAAAGTT
* * * *
11494 AATTATTTTTAGAGAAATATTTTAT
131 AATCATTTTTACAGAAATATTATAG
*
11519 TAATATTTATTTATTTTTTAATATTAAGAAAATGACTGTCTTAAAGCAACTAGAAGTCTTTTTCT
1 TAATATTTATTTATTTTTTAATATTAAGAAAATGACTGTCTTAAAGCAACTAGAAGTCCTTTTCT
* *
11584 GATATTTCTAAGTAAATAAATATTTTA-TTTATAAAAATAAAAAATATATATATATTT-ATAAAA
66 GATATTTCTAAATAAATAAATATCTTACTTT-TAAAAATAAAAAATATAT-TA-ATTTAATAAAA
**
11647 GTTAATACATTTTT-CTTAAA-ATTATAG
128 GTTAAT-CATTTTTACAGAAATATTATAG
11674 TAATA
1 TAATA
11679 AATTTGAAAT
Statistics
Matches: 136, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
154 3 0.02
155 110 0.81
156 13 0.10
157 10 0.07
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (155 bp):
TAATATTTATTTATTTTTTAATATTAAGAAAATGACTGTCTTAAAGCAACTAGAAGTCCTTTTCT
GATATTTCTAAATAAATAAATATCTTACTTTTAAAAATAAAAAATATATTAATTTAATAAAAGTT
AATCATTTTTACAGAAATATTATAG
Found at i:20292 original size:64 final size:63
Alignment explanation
Indices: 20220--20362 Score: 187
Period size: 64 Copynumber: 2.2 Consensus size: 63
20210 ATGCACAGGA
* *
20220 AGTGCATCGATGCACCCATTAAAAATGGAAACATCGAATGCAATTAGTGCATCGATGCATAAGG
1 AGTGCATCGATGCACCCATT-AAAATGAAAACATCGAAGGCAATTAGTGCATCGATGCATAAGG
* ** * * * *
20284 AGTGCATCGATGCACCCCCTTAAAATGAAAACATCGAAGGTGATTTGTGTATCGATGCATGAGT
1 AGTGCATCGATGCA-CCCATTAAAATGAAAACATCGAAGGCAATTAGTGCATCGATGCATAAGG
20348 AGTGCATCGATGCAC
1 AGTGCATCGATGCAC
20363 ATGTTAAAGA
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
63 1 0.01
64 63 0.91
65 5 0.07
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.24
Consensus pattern (63 bp):
AGTGCATCGATGCACCCATTAAAATGAAAACATCGAAGGCAATTAGTGCATCGATGCATAAGG
Found at i:21109 original size:23 final size:23
Alignment explanation
Indices: 21061--21140 Score: 103
Period size: 23 Copynumber: 3.6 Consensus size: 23
21051 GGGTCTACGC
*
21061 GGTCCTTCGGGACA--T-ACAGT
1 GGTCCTTCGGGACATTTCATAGT
* * *
21081 GATCCTTCGGGATATTTTATAGT
1 GGTCCTTCGGGACATTTCATAGT
21104 GGTCCTTCGGGACATTTCATAGT
1 GGTCCTTCGGGACATTTCATAGT
21127 GGTCCTTCGGGACA
1 GGTCCTTCGGGACA
21141 AATCTCAAAG
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.24
22 1 0.02
23 38 0.75
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.33
Consensus pattern (23 bp):
GGTCCTTCGGGACATTTCATAGT
Found at i:25333 original size:19 final size:18
Alignment explanation
Indices: 25309--25357 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
25299 ATGCTTGAAG
25309 AAGAAAAAATAAAAAAAGA
1 AAGAAAAAATAAAAAAA-A
*
25328 AAG-AAAAA-AAACAAAA
1 AAGAAAAAATAAAAAAAA
*
25344 AACAAAAAATAAAA
1 AAGAAAAAATAAAA
25358 TAGAAAATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 3 0.12
17 11 0.44
18 8 0.32
19 3 0.12
ACGTcount: A:0.86, C:0.04, G:0.06, T:0.04
Consensus pattern (18 bp):
AAGAAAAAATAAAAAAAA
Found at i:25337 original size:20 final size:20
Alignment explanation
Indices: 25312--25364 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
25302 CTTGAAGAAG
*
25312 AAAAAATA-AAAAAAGAAAGA
1 AAAAAATACAAAAAACAAA-A
25332 AAAAAA-ACAAAAAACAAAA
1 AAAAAATACAAAAAACAAAA
*
25351 AATAAAATAGAAAA
1 AA-AAAATACAAAA
25365 TGAGGGTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 4 0.14
20 19 0.68
21 5 0.18
ACGTcount: A:0.85, C:0.04, G:0.06, T:0.06
Consensus pattern (20 bp):
AAAAAATACAAAAAACAAAA
Found at i:25738 original size:18 final size:18
Alignment explanation
Indices: 25712--25749 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
25702 CAAGTTTATC
*
25712 TTTTTGAAATTCAATTTA
1 TTTTCGAAATTCAATTTA
25730 TTTTCGAAATTCAATTTA
1 TTTTCGAAATTCAATTTA
25748 TT
1 TT
25750 CTTTTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.55
Consensus pattern (18 bp):
TTTTCGAAATTCAATTTA
Found at i:26400 original size:22 final size:21
Alignment explanation
Indices: 26372--26480 Score: 130
Period size: 22 Copynumber: 5.0 Consensus size: 21
26362 CTACATCTAC
26372 ATTCTTCAAAGATGATAGATAT
1 ATTCTTCAAAGATGATAGAT-T
*
26394 ATTCTTCAAAGATGATAAATT
1 ATTCTTCAAAGATGATAGATT
*
26415 CTCTCTTCAAAGATGATAGATT
1 AT-TCTTCAAAGATGATAGATT
26437 ATCTCTTCAAAGATGATAGATTCT
1 AT-TCTTCAAAGATGATAGA-T-T
* *
26461 ATT-TTCAAAGAAGAAAGATT
1 ATTCTTCAAAGATGATAGATT
26481 TATTGGATTT
Statistics
Matches: 78, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
20 1 0.01
21 3 0.04
22 69 0.88
23 2 0.03
24 3 0.04
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (21 bp):
ATTCTTCAAAGATGATAGATT
Found at i:26431 original size:44 final size:44
Alignment explanation
Indices: 26374--26480 Score: 153
Period size: 44 Copynumber: 2.4 Consensus size: 44
26364 ACATCTACAT
*
26374 TCTTCAAAGATGATAGATATAT-TCTTCAAAGATGATAAATTCTC
1 TCTTCAAAGATGATAGAT-TATCTCTTCAAAGATGATAAATTCTA
*
26418 TCTTCAAAGATGATAGATTATCTCTTCAAAGATGATAGATTCTA
1 TCTTCAAAGATGATAGATTATCTCTTCAAAGATGATAAATTCTA
* * *
26462 TTTTCAAAGAAGAAAGATT
1 TCTTCAAAGATGATAGATT
26481 TATTGGATTT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
43 3 0.05
44 54 0.95
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (44 bp):
TCTTCAAAGATGATAGATTATCTCTTCAAAGATGATAAATTCTA
Found at i:27046 original size:38 final size:38
Alignment explanation
Indices: 26996--27089 Score: 136
Period size: 38 Copynumber: 2.5 Consensus size: 38
26986 AAACATTTCC
*
26996 AGAAGTGTTCATAATGAGAAAAACTCATCTGAAGAGG-
1 AGAAGAGTTCATAATGAGAAAAACTCATCTGAAGAGGA
* *
27033 AGAAGAAGTTCATAATGAGAAGAACTCGTCTGAAGAGGA
1 AGAAG-AGTTCATAATGAGAAAAACTCATCTGAAGAGGA
*
27072 AGAAGAGGTCATAATGAG
1 AGAAGAGTTCATAATGAG
27090 CAGAACTTGT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
37 5 0.10
38 41 0.80
39 5 0.10
ACGTcount: A:0.44, C:0.10, G:0.28, T:0.19
Consensus pattern (38 bp):
AGAAGAGTTCATAATGAGAAAAACTCATCTGAAGAGGA
Found at i:27257 original size:123 final size:122
Alignment explanation
Indices: 27038--27298 Score: 416
Period size: 123 Copynumber: 2.1 Consensus size: 122
27028 AGAGGAGAAG
* * *
27038 AAGTTCATAATGAGAAGAACTCGTCTGAAGAGGAAGAAGAGGTCATAATGAGCAGAACTTGTTCA
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTCATAATGAGAAGAACTTGTTCA
* *
27103 ACCTTTTGCATGATTCTATCACAGAAGGAGATAGATCAGCATCAACTTTTCCAGAGA
66 ACCATTTGCATGATTCTATCACAGAAGGAGATAGATCAACATCAACTTTTCCAGAGA
* * *
27160 AAGTTTATAATGAGAAGAACTCATTTGAAGAAGG-AGAAGAAATTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAG-AAGTCATAATGAGAAGAACTTGTT
*
27224 CAACCATTTGCATGATTCTATCACAGAATGAGATAGATCAACATCAACTTTTCCAGAGA
64 CAACCATTTGCATGATTCTATCACAGAAGGAGATAGATCAACATCAACTTTTCCAGAGA
27283 AAGTTCATAATGAGAA
1 AAGTTCATAATGAGAA
27299 AAATTTGTTC
Statistics
Matches: 127, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
122 32 0.25
123 95 0.75
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.26
Consensus pattern (122 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTCATAATGAGAAGAACTTGTTCA
ACCATTTGCATGATTCTATCACAGAAGGAGATAGATCAACATCAACTTTTCCAGAGA
Found at i:27295 original size:84 final size:83
Alignment explanation
Indices: 27196--27388 Score: 271
Period size: 84 Copynumber: 2.3 Consensus size: 83
27186 GAAGAAGGAG
* *
27196 AAGAAATTCATAATGAGAAGAACTTGTTCAACCATTTGCATGATTCTATCACAGAATGAGATAGA
1 AAGAAATTCATAATGAGAAGAACTTGTTCAACCATTTGCATGACTCTATCACAGAAAGAGATAGA
*
27261 TCAACA-TCAACTTTTCCA
66 TCAACACT-AACATTTCCA
* * * * *
27279 GAGAAAGTTCATAATGAGAAAAATTTGTTCAACCTTTTGCTTGACTCTATCACAGAAAGAGATAG
1 AAGAAA-TTCATAATGAGAAGAACTTGTTCAACCATTTGCATGACTCTATCACAGAAAGAGATAG
27344 ATCAACACTAACATTTCCA
65 ATCAACACTAACATTTCCA
*
27363 AATAAATTTCATAATGAGAAGAACTT
1 AAGAAA-TTCATAATGAGAAGAACTT
27389 ATCTGAAGAG
Statistics
Matches: 95, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
83 5 0.05
84 89 0.94
85 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.29
Consensus pattern (83 bp):
AAGAAATTCATAATGAGAAGAACTTGTTCAACCATTTGCATGACTCTATCACAGAAAGAGATAGA
TCAACACTAACATTTCCA
Found at i:27790 original size:3 final size:3
Alignment explanation
Indices: 27784--27883 Score: 134
Period size: 3 Copynumber: 34.0 Consensus size: 3
27774 TCATTTGGTT
27784 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
27831 TTA TTG TTA TTA TTA TT- TTAA TTA -TA ATA ATA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
27875 TTA TTA TTA
1 TTA TTA TTA
27884 CAGGCCCAAA
Statistics
Matches: 90, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
2 6 0.07
3 82 0.91
4 2 0.02
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:43019 original size:2 final size:2
Alignment explanation
Indices: 43008--43054 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
42998 GTTTTATTAT
43008 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43049 TA TA TA
1 TA TA TA
43055 CTAATAAGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:51522 original size:20 final size:20
Alignment explanation
Indices: 51450--51547 Score: 126
Period size: 20 Copynumber: 4.9 Consensus size: 20
51440 TTCCCAGTAC
*
51450 TTTGTAAAGCC-TCTGGGTCA
1 TTTGTAAAGCCTTC-GGGTAA
* *
51470 TTTGTAAAGCCTCCGGGTCA
1 TTTGTAAAGCCTTCGGGTAA
51490 TTTGTAAAGCCTTCGGGTAA
1 TTTGTAAAGCCTTCGGGTAA
**
51510 TTTGTAAAGCCTTAAGGTAA
1 TTTGTAAAGCCTTCGGGTAA
*
51530 TTTGTAAATCCTTCGGGT
1 TTTGTAAAGCCTTCGGGT
51548 CATCTGTTAG
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 68 0.99
21 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
TTTGTAAAGCCTTCGGGTAA
Found at i:52706 original size:2 final size:2
Alignment explanation
Indices: 52699--52728 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
52689 GGTCACTATC
52699 AT AT AT AT AT 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
52729 TAGGATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56136 original size:22 final size:22
Alignment explanation
Indices: 56108--56158 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
56098 CATCATACTT
56108 ATATATATAGTATTTGTAAATA
1 ATATATATAGTATTTGTAAATA
56130 ATATATATAGTATTTGTAAATA
1 ATATATATAGTATTTGTAAATA
56152 ATATATA
1 ATATATA
56159 AAAGAAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (22 bp):
ATATATATAGTATTTGTAAATA
Found at i:56375 original size:25 final size:26
Alignment explanation
Indices: 56354--56404 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
56344 ATTTATTATT
56354 TTTAGAATT-TAATAAAAATATTAAA
1 TTTAGAATTGTAATAAAAATATTAAA
* *
56379 TTTATAATTGGTAATAAAAAAATTAA
1 TTTAGAATT-GTAATAAAAATATTAA
56405 TAAAATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 8 0.36
27 14 0.64
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (26 bp):
TTTAGAATTGTAATAAAAATATTAAA
Found at i:56818 original size:11 final size:11
Alignment explanation
Indices: 56802--56826 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
56792 CTATTAATCC
56802 GACCCGATATT
1 GACCCGATATT
56813 GACCCGATATT
1 GACCCGATATT
56824 GAC
1 GAC
56827 ACAATCCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (11 bp):
GACCCGATATT
Found at i:60985 original size:16 final size:16
Alignment explanation
Indices: 60966--61024 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
60956 TGAACTGAAA
60966 TCAACCCGAACCGAAG
1 TCAACCCGAACCGAAG
* *
60982 TCAACCCTAATCGAAAG
1 TCAACCCGAACCG-AAG
* *
60999 -CAACTCGAACCAAAAG
1 TCAACCCGAACC-GAAG
61015 T-AACCCGAAC
1 TCAACCCGAAC
61025 TAAAATCAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
16 30 0.91
17 3 0.09
ACGTcount: A:0.42, C:0.34, G:0.14, T:0.10
Consensus pattern (16 bp):
TCAACCCGAACCGAAG
Found at i:61790 original size:46 final size:45
Alignment explanation
Indices: 61738--61847 Score: 141
Period size: 46 Copynumber: 2.4 Consensus size: 45
61728 ATGGTTGAAA
61738 CAAACCAAAATCAACTTGAATTGA-CTCAAAAATCTAAAGGTTGACC
1 CAAACCAAAA-CAACTTGAATTGACCT-AAAAATCTAAAGGTTGACC
* * * *
61784 CGAACCAAAACCGACCTGAATTGACCTGAAAATCTAAAGGTTGACC
1 CAAACCAAAA-CAACTTGAATTGACCTAAAAATCTAAAGGTTGACC
*
61830 CAAACCAAAACAAATTGA
1 CAAACCAAAACAACTTGA
61848 CCGATACTAA
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
45 5 0.09
46 47 0.87
47 2 0.04
ACGTcount: A:0.45, C:0.24, G:0.13, T:0.18
Consensus pattern (45 bp):
CAAACCAAAACAACTTGAATTGACCTAAAAATCTAAAGGTTGACC
Found at i:61905 original size:32 final size:32
Alignment explanation
Indices: 61867--61957 Score: 121
Period size: 32 Copynumber: 2.8 Consensus size: 32
61857 ACCCAACTCG
* * *
61867 AAACCAACCGATCTGATATTAACCCGA-CTGAA
1 AAACCAATCGATCCGATTTTAACCCGACCT-AA
* *
61899 AAACCAATTGATCCGATTTTAACTCGACCTAA
1 AAACCAATCGATCCGATTTTAACCCGACCTAA
61931 AAACCAATCGATCCGATTTTAACCCGA
1 AAACCAATCGATCCGATTTTAACCCGA
61958 ACCCGATCTG
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
32 49 0.96
33 2 0.04
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.23
Consensus pattern (32 bp):
AAACCAATCGATCCGATTTTAACCCGACCTAA
Found at i:62298 original size:15 final size:15
Alignment explanation
Indices: 62278--62309 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
62268 TTTCAGTTTG
62278 AAAAAAACCGATTAT
1 AAAAAAACCGATTAT
62293 AAAAAAACCGATTAT
1 AAAAAAACCGATTAT
62308 AA
1 AA
62310 TATTATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (15 bp):
AAAAAAACCGATTAT
Found at i:62387 original size:32 final size:32
Alignment explanation
Indices: 62351--62427 Score: 127
Period size: 33 Copynumber: 2.4 Consensus size: 32
62341 ACAAAGTTTA
*
62351 CGATAATTGAAATACTTAAATACTTCCAAGTT
1 CGATAATTGAAATACTTAAAAACTTCCAAGTT
*
62383 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGAT-AATTGAAATACTTAAAAACTTCCAAGTT
62416 CGATAATTGAAA
1 CGATAATTGAAA
62428 CAAAGTTTAC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 11 0.27
33 30 0.73
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (32 bp):
CGATAATTGAAATACTTAAAAACTTCCAAGTT
Found at i:62441 original size:21 final size:21
Alignment explanation
Indices: 62416--62457 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
62406 CTTCCAAGTT
62416 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
62437 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
62458 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:70247 original size:2 final size:2
Alignment explanation
Indices: 70235--70277 Score: 77
Period size: 2 Copynumber: 21.0 Consensus size: 2
70225 GCTGACTTCC
70235 AG AG TAG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG -AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
70278 GAAAGGGGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.02
Consensus pattern (2 bp):
AG
Done.