Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005623.1 Hibiscus syriacus cultivar Beakdansim tig00013093_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: 56425
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:8247 original size:14 final size:14
Alignment explanation
Indices: 8228--8290 Score: 94
Period size: 14 Copynumber: 4.5 Consensus size: 14
8218 TACACCTAAG
8228 AAGAAAAAAA-AATA
1 AAGAAAAAAAGAA-A
8242 AAGAAAAACAAGAAA
1 AAGAAAAA-AAGAAA
8257 AAGAAAAAAA-AAA
1 AAGAAAAAAAGAAA
8270 AAGAAAAAAAGAAA
1 AAGAAAAAAAGAAA
8284 AAGAAAA
1 AAGAAAA
8291 TGAGAGGTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
13 13 0.28
14 20 0.43
15 11 0.24
16 2 0.04
ACGTcount: A:0.86, C:0.02, G:0.11, T:0.02
Consensus pattern (14 bp):
AAGAAAAAAAGAAA
Found at i:8254 original size:9 final size:9
Alignment explanation
Indices: 8225--8285 Score: 63
Period size: 9 Copynumber: 6.9 Consensus size: 9
8215 TATTACACCT
*
8225 AAGAAGAAA
1 AAGAAAAAA
*
8234 AA-AAAATA
1 AAGAAAAAA
*
8242 AAGAAAAAC
1 AAGAAAAAA
8251 AAGAAAAAGA
1 AAGAAAAA-A
*
8261 AAAAAAAAA
1 AAGAAAAAA
8270 AAG-AAAAA
1 AAGAAAAAA
8278 AAGAAAAA
1 AAGAAAAA
8286 GAAAATGAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
8 14 0.33
9 21 0.50
10 7 0.17
ACGTcount: A:0.85, C:0.02, G:0.11, T:0.02
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:8262 original size:6 final size:6
Alignment explanation
Indices: 8251--8290 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
8241 AAAGAAAAAC
*
8251 AAGAAA AAGAAA AA-AAA AA-AAG AA-AAA AAGAAA AAGAAA A
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA A
8291 TGAGAGGTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 13 0.42
6 18 0.58
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:8276 original size:27 final size:29
Alignment explanation
Indices: 8228--8290 Score: 103
Period size: 27 Copynumber: 2.2 Consensus size: 29
8218 TACACCTAAG
*
8228 AAGAAAAAAAAATAAAGAAAAACAAGAAA
1 AAGAAAAAAAAATAAAGAAAAAAAAGAAA
8257 AAGAAAAAAAAA-AAAG-AAAAAAAGAAA
1 AAGAAAAAAAAATAAAGAAAAAAAAGAAA
8284 AAGAAAA
1 AAGAAAA
8291 TGAGAGGTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
27 17 0.52
28 4 0.12
29 12 0.36
ACGTcount: A:0.86, C:0.02, G:0.11, T:0.02
Consensus pattern (29 bp):
AAGAAAAAAAAATAAAGAAAAAAAAGAAA
Found at i:8364 original size:24 final size:23
Alignment explanation
Indices: 8337--8412 Score: 134
Period size: 24 Copynumber: 3.2 Consensus size: 23
8327 TGAAACCAAG
8337 GAAGGATTTGAGTTGAAAACCCA
1 GAAGGATTTGAGTTGAAAACCCA
8360 TGAAGGATTTGAGTTGAAAACCCAA
1 -GAAGGATTTGAGTTGAAAACCC-A
8385 GAAGGATTTGAGTTGAAAACCCA
1 GAAGGATTTGAGTTGAAAACCCA
8408 GAAGG
1 GAAGG
8413 GCGGTTCAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
23 6 0.12
24 44 0.86
25 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.28, T:0.21
Consensus pattern (23 bp):
GAAGGATTTGAGTTGAAAACCCA
Found at i:9540 original size:136 final size:135
Alignment explanation
Indices: 9279--9855 Score: 717
Period size: 136 Copynumber: 4.2 Consensus size: 135
9269 AACCGATCAA
* * *
9279 TTTCAAATGGAGAGTTTATATTGAGAAGAACTTATCCGACAAAGGGAGAAGAAGTTCATAATGAG
1 TTTC-AATGGAGAGTTCATAATGAGAAGAACTTATCCGACAGAGGGAGAAGAAGTTCATAATGAG
* * * ** * *
9344 AAGAGCTTGTTCGACCTATCGCTTGATTCACGGTATTTCGAATTAGTGACGCCTCGCTTGAGGGA
65 AAGAGCTTGTTCAACCTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTGAGGGA
*
9409 TTGATGT
130 TTGA-AT
*
9416 TTTCAATGAAGAGTTCATAATGAGAAGAACTTATCCGACAGAGGGAGAAGAAGTTCATAATGAGA
1 TTTCAATGGAGAGTTCATAATGAGAAGAACTTATCCGACAGAGGGAGAAGAAGTTCATAATGAGA
* * ** *
9481 AGAGCTTGTTCAATCTATCACTCGATTTACGACATTTTAAATCAGTGACACCAT-ACTTGAGGGA
66 AGAGCTTGTTCAACCTATCACTCGATTCACGACATTTCGAATCAGTGACACC-TCGCTTGAGGGA
9545 TTGAAAT
130 TTG-AAT
* ** * * *
9552 TTTCAATGAAGAGTTCATAATGAGAAGAACTCGTCTGACAGAGGGAGAAAAAGTTCATTATGAGA
1 TTTCAATGGAGAGTTCATAATGAGAAGAACTTATCCGACAGAGGGAGAAGAAGTTCATAATGAGA
* * * * * * *
9617 AGAGCTTGTTCAACCTTTCACTCAATCCATGACATTTTGAATCAGTAACACCTCGCTTTAGGGAT
66 AGAGCTTGTTCAACCTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTGAGGGAT
9682 TGACA-
131 TGA-AT
* ** * *
9687 TTTCAAATGGAGAGTTCATAATGAGAAGAACTCATATGAAAGAGGGAGAAGAAATTCATAATGAG
1 TTTC-AATGGAGAGTTCATAATGAGAAGAACTTATCCGACAGAGGGAGAAGAAGTTCATAATGAG
* * *
9752 AAGATCTTGTTCAACCTATCACTCGATTCACGGCATTTCGAATCAGTGATACCTCGCTTGAGGGA
65 AAGAGCTTGTTCAACCTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTGAGGGA
9817 TTGACAT
130 TTGA-AT
* *
9824 TTTCGATGGAGAGTTCATATTGAGAAGAACTT
1 TTTCAATGGAGAGTTCATAATGAGAAGAACTT
9856 GTTCGACCTA
Statistics
Matches: 382, Mismatches: 52, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
135 6 0.02
136 366 0.96
137 10 0.03
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (135 bp):
TTTCAATGGAGAGTTCATAATGAGAAGAACTTATCCGACAGAGGGAGAAGAAGTTCATAATGAGA
AGAGCTTGTTCAACCTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTGAGGGAT
TGAAT
Found at i:9920 original size:96 final size:96
Alignment explanation
Indices: 9741--9921 Score: 220
Period size: 96 Copynumber: 1.9 Consensus size: 96
9731 GGAGAAGAAA
* ** * **
9741 TTCATAATGAGAAGATCTTGTTCAACCTATCACTCGATTCACGGCATTTCGAATCAGTGATACCT
1 TTCATAATGAGAAGAACTTGTTCAACCTATCACTCGATTCACAACACTTCGAATCAGCCATACCT
* **
9806 CGCTTGAGGGATTGACATTTTCGATGGAGAG
66 CACTTGAGGGATCAACATTTTCGATGGAGAG
* * ** *
9837 TTCATATTGAGAAGAACTTGTTCGACCTATTGCTCGATTCACAACACTTCGAATTAGCCATACCT
1 TTCATAATGAGAAGAACTTGTTCAACCTATCACTCGATTCACAACACTTCGAATCAGCCATACCT
9902 CACTAT-AGGGATCAACATTT
66 CACT-TGAGGGATCAACATTT
9922 CCAAAAGAAC
Statistics
Matches: 70, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
96 69 0.99
97 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (96 bp):
TTCATAATGAGAAGAACTTGTTCAACCTATCACTCGATTCACAACACTTCGAATCAGCCATACCT
CACTTGAGGGATCAACATTTTCGATGGAGAG
Found at i:10139 original size:24 final size:22
Alignment explanation
Indices: 10112--10164 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 22
10102 AAGCCCAACC
10112 AAACCCAGA-CCCATAACCAAGCTA
1 AAACCCA-ACCCCA-AACCAA-CTA
*
10136 AAACCTCAACCCCAAACCAATTA
1 AAACC-CAACCCCAAACCAACTA
10159 AAACCC
1 AAACCC
10165 CTAAACTCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 1 0.04
23 7 0.27
24 12 0.46
25 6 0.23
ACGTcount: A:0.47, C:0.40, G:0.04, T:0.09
Consensus pattern (22 bp):
AAACCCAACCCCAAACCAACTA
Found at i:11631 original size:10 final size:10
Alignment explanation
Indices: 11618--11653 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
11608 TTTATGTTTA
11618 TTTTTTTTTG
1 TTTTTTTTTG
* *
11628 TTTTTTGTTA
1 TTTTTTTTTG
11638 TTTTTTTTTG
1 TTTTTTTTTG
11648 TTTTTT
1 TTTTTT
11654 AATTTGATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.03, C:0.00, G:0.08, T:0.89
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:11640 original size:20 final size:20
Alignment explanation
Indices: 11615--11653 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
11605 ATATTTATGT
11615 TTATTTTTTTTTGTTTTTTG
1 TTATTTTTTTTTGTTTTTTG
11635 TTATTTTTTTTTGTTTTTT
1 TTATTTTTTTTTGTTTTTT
11654 AATTTGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.05, C:0.00, G:0.08, T:0.87
Consensus pattern (20 bp):
TTATTTTTTTTTGTTTTTTG
Found at i:19883 original size:21 final size:22
Alignment explanation
Indices: 19841--19884 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
19831 GAATGAATAT
* *
19841 TCTAGATCATTTTGAGGATGAA
1 TCTAGATCAATTTGAAGATGAA
*
19863 TCTAGA-CAATTTGAAGCTGAA
1 TCTAGATCAATTTGAAGATGAA
19884 T
1 T
19885 TTGGCCTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (22 bp):
TCTAGATCAATTTGAAGATGAA
Found at i:20463 original size:18 final size:18
Alignment explanation
Indices: 20426--20494 Score: 95
Period size: 18 Copynumber: 3.9 Consensus size: 18
20416 AATTAAGAGT
**
20426 TAGTTTAAGAAATG-AAC
1 TAGTTTAATTAATGAAAC
* *
20443 TAGTTTGATGAATGAAAC
1 TAGTTTAATTAATGAAAC
20461 TAGTTTAATTAATGAAAC
1 TAGTTTAATTAATGAAAC
20479 TAGTTTAATTAATGAA
1 TAGTTTAATTAATGAA
20495 CTAACTTTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
17 11 0.24
18 35 0.76
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.36
Consensus pattern (18 bp):
TAGTTTAATTAATGAAAC
Found at i:20465 original size:35 final size:35
Alignment explanation
Indices: 20426--20545 Score: 111
Period size: 35 Copynumber: 3.4 Consensus size: 35
20416 AATTAAGAGT
*
20426 TAGTTTAAGAAATGAACTAGTTTGATGAATGAAAC
1 TAGTTTAATAAATGAACTAGTTTGATGAATGAAAC
* * *
20461 TAGTTTAATTAATGAAACTAGTTTAATTAATG-AAC
1 TAGTTTAATAAATG-AACTAGTTTGATGAATGAAAC
* * *
20496 TAACTTTATTAAATGAACTAG-ATGCATGAATGAAA-
1 T-AGTTTAATAAATGAACTAGTTTG-ATGAATGAAAC
* *
20531 TAGCTTACTAAATGA
1 TAGTTTAATAAATGA
20546 TCTAAATGCA
Statistics
Matches: 68, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
34 12 0.18
35 29 0.43
36 27 0.40
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.34
Consensus pattern (35 bp):
TAGTTTAATAAATGAACTAGTTTGATGAATGAAAC
Found at i:20503 original size:18 final size:18
Alignment explanation
Indices: 20464--20515 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
20454 ATGAAACTAG
*
20464 TTTAATTAATGAAACT-AG
1 TTTAATTAATG-AACTAAC
20482 TTTAATTAATGAACTAAC
1 TTTAATTAATGAACTAAC
20500 TTT-ATTAAATGAACTA
1 TTTAATT-AATGAACTA
20516 GATGCATGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 7 0.23
18 24 0.77
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (18 bp):
TTTAATTAATGAACTAAC
Found at i:21873 original size:17 final size:17
Alignment explanation
Indices: 21851--21888 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
21841 GACCGGTTCC
21851 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
21868 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
21885 GACC
1 GACC
21889 GTTGATCGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.47, G:0.24, T:0.11
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:21969 original size:29 final size:29
Alignment explanation
Indices: 21896--21963 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
21886 ACCGTTGATC
* *
21896 GGTGCTATTTTAGTAATTAATTCAAAATA
1 GGTGCTATTTTAGTAATTAATTAAAAAGA
*
21925 GGTACTATTTTAGTAATTAATTTAAAAAGA
1 GGTGCTATTTTAGTAATTAA-TTAAAAAGA
21955 GGTGCTATT
1 GGTGCTATT
21964 CAGTAAAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 19 0.56
30 15 0.44
ACGTcount: A:0.37, C:0.06, G:0.16, T:0.41
Consensus pattern (29 bp):
GGTGCTATTTTAGTAATTAATTAAAAAGA
Found at i:22897 original size:42 final size:41
Alignment explanation
Indices: 22838--23004 Score: 280
Period size: 42 Copynumber: 4.0 Consensus size: 41
22828 GGAAGTATTA
22838 CCAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTC
1 CCAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTC
*
22880 CCAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTA
1 CCAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTC
22922 CCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTC
1 CCAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTC
*
22964 CCAGGTCCCTTTGCTGTGTGCAAGGATAAACCTTACAGTTT
1 CCAGGTCCCTTTGCTGTGTGCAAGG-TAAGCCTTACAGTTT
23005 TCCTAGGCTC
Statistics
Matches: 120, Mismatches: 3, Indels: 4
0.94 0.02 0.03
Matches are distributed among these distances:
41 4 0.03
42 116 0.97
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.31
Consensus pattern (41 bp):
CCAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTC
Found at i:29212 original size:29 final size:29
Alignment explanation
Indices: 29170--29225 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
29160 ACCGTTGATC
*
29170 GGTGTTATTTTAGTAATTAATTCAAAATA
1 GGTGATATTTTAGTAATTAATTCAAAATA
*
29199 GGTGATATTTTAGTAATTAATTTAAAA
1 GGTGATATTTTAGTAATTAATTCAAAA
29226 AGAGGTGCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.39, C:0.02, G:0.14, T:0.45
Consensus pattern (29 bp):
GGTGATATTTTAGTAATTAATTCAAAATA
Found at i:29238 original size:30 final size:29
Alignment explanation
Indices: 29170--29238 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
29160 ACCGTTGATC
* * *
29170 GGTGTTATTTTAGTAATTAATTCAAAATA
1 GGTGATATTTTAGTAATTAATTAAAAAGA
29199 GGTGATATTTTAGTAATTAATTTAAAAAGA
1 GGTGATATTTTAGTAATTAA-TTAAAAAGA
*
29229 GGTGCTATTT
1 GGTGATATTT
29239 CTGTAAAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
29 19 0.54
30 16 0.46
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.43
Consensus pattern (29 bp):
GGTGATATTTTAGTAATTAATTAAAAAGA
Found at i:30184 original size:42 final size:41
Alignment explanation
Indices: 30124--30290 Score: 262
Period size: 42 Copynumber: 4.0 Consensus size: 41
30114 GGAAGTATTA
30124 CCAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTC
1 CCAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTC
* *
30166 CCAGGTCCCTTTGTTGTGTGCGAAGGTAAGCCTTACAGTTTA
1 CCAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTC
*
30208 CCAGGTCCCTTTGCTGTTTGCAAGGGTAAGCCTTACAGTTTC
1 CCAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTC
*
30250 CCAGGTCCCTTTGCTGTGTGCAAGGATAACCCTTACAGTTT
1 CCAGGTCCCTTTGCTGTGTGCAAGG-TAAGCCTTACAGTTT
30291 TCCTAGGCTC
Statistics
Matches: 116, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
41 4 0.03
42 112 0.97
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (41 bp):
CCAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTC
Found at i:33996 original size:122 final size:121
Alignment explanation
Indices: 33861--34143 Score: 372
Period size: 122 Copynumber: 2.3 Consensus size: 121
33851 CTTTGTAATG
* * ** **
33861 AGGAAATTGGGTCAATCCGGAGAT-ATTACGGTGTTGAAGACGACTCTGGTCATCTGTGTTAAAG
1 AGGAAATTGGGTCAATCTGGAGATAATT-TGGTGTTGAAGACGACTCTACTCATCCATGTTAAAG
* * * *
33925 AGTTCTAGCTGCTTTCAGGTAAATTGTTTGTTGAAGATGACATTGTTCCTTCT-TGTT
65 AGATCTAGCTGCTTTCAGATAAATTGTTTGTTGAAGATGACATTGTTCATTATCT-TT
* *
33982 AAGGAAGTTGGGTCAATCTGGAGATAATTTGGTGTTGAAGACGACTCTACTCATCCATGTTGAAG
1 -AGGAAATTGGGTCAATCTGGAGATAATTTGGTGTTGAAGACGACTCTACTCATCCATGTTAAAG
* * * *
34047 AGATCTGGTTGCTTTCAGATAAATTGTTTGTTGAAGATGACGTTTTTCATTATCTTT
65 AGATCTAGCTGCTTTCAGATAAATTGTTTGTTGAAGATGACATTGTTCATTATCTTT
*
34104 AGGAAATCGGGTCAATCTGGAGATAATTTGGTGTTGAAGA
1 AGGAAATTGGGTCAATCTGGAGATAATTTGGTGTTGAAGA
34144 AGTTCTAGAA
Statistics
Matches: 141, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
121 38 0.27
122 99 0.70
123 4 0.03
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.36
Consensus pattern (121 bp):
AGGAAATTGGGTCAATCTGGAGATAATTTGGTGTTGAAGACGACTCTACTCATCCATGTTAAAGA
GATCTAGCTGCTTTCAGATAAATTGTTTGTTGAAGATGACATTGTTCATTATCTTT
Found at i:35316 original size:5 final size:6
Alignment explanation
Indices: 35302--35370 Score: 51
Period size: 6 Copynumber: 12.2 Consensus size: 6
35292 TCTGTCCTTA
*
35302 TTTTCT TTTTCT TTTTCAT TTTTC- --TTCT TTTTAT TTTTC- TTTT-T
1 TTTTCT TTTTCT TTTTC-T TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
* *
35346 TCTTCT TTTT-T TGTTTCA TTTTCT T
1 TTTTCT TTTTCT T-TTTCT TTTTCT T
35371 CTATTCAGGT
Statistics
Matches: 49, Mismatches: 6, Indels: 16
0.69 0.08 0.23
Matches are distributed among these distances:
3 3 0.06
5 9 0.18
6 30 0.61
7 7 0.14
ACGTcount: A:0.04, C:0.14, G:0.01, T:0.80
Consensus pattern (6 bp):
TTTTCT
Found at i:35332 original size:22 final size:21
Alignment explanation
Indices: 35304--35372 Score: 95
Period size: 22 Copynumber: 3.2 Consensus size: 21
35294 TGTCCTTATT
35304 TTCTTTTTCTTTTTCATTTTTC
1 TTCTTTTT-TTTTTCATTTTTC
*
35326 TTCTTTTTATTTTTCTTTTTTC
1 TTCTTTTT-TTTTTCATTTTTC
35348 TTCTTTTTTTGTTTCA-TTTTC
1 TTCTTTTTTT-TTTCATTTTTC
35369 TTCT
1 TTCT
35373 ATTCAGGTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
21 11 0.26
22 32 0.74
ACGTcount: A:0.04, C:0.16, G:0.01, T:0.78
Consensus pattern (21 bp):
TTCTTTTTTTTTTCATTTTTC
Found at i:35355 original size:16 final size:16
Alignment explanation
Indices: 35310--35346 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
35300 TATTTTCTTT
35310 TTCTTTTTCATTTTTC
1 TTCTTTTTCATTTTTC
35326 TTCTTTTT-ATTTTTC
1 TTCTTTTTCATTTTTC
35341 TT-TTTT
1 TTCTTTT
35347 CTTCTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 4 0.19
15 9 0.43
16 8 0.38
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (16 bp):
TTCTTTTTCATTTTTC
Found at i:41894 original size:77 final size:79
Alignment explanation
Indices: 41762--41914 Score: 215
Period size: 77 Copynumber: 2.0 Consensus size: 79
41752 ATATAGTAGG
*
41762 TAAACATTAAAAGAATGTAATTTTGATTACAACTCTTTTAATTGATATTTAATTTGGAA-TAATT
1 TAAACATTAAAAGAATGTAATTTAGATTACAACTCTTTTAATTGATATTTAATTT-GAATTAATT
41826 AAATAAGATTTTAAA
65 AAATAAGATTTTAAA
** * *
41841 TAAACATT-AAAGGGTGTAATTTAGATTATAAGTC-TTTAA-TGTATATTTAATTTGAATTAATT
1 TAAACATTAAAAGAATGTAATTTAGATTACAACTCTTTTAATTG-ATATTTAATTTGAATTAATT
41903 AAATAAGATTTT
65 AAATAAGATTTT
41915 TATTAATTCA
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
76 5 0.07
77 33 0.49
78 21 0.31
79 8 0.12
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.43
Consensus pattern (79 bp):
TAAACATTAAAAGAATGTAATTTAGATTACAACTCTTTTAATTGATATTTAATTTGAATTAATTA
AATAAGATTTTAAA
Found at i:49940 original size:11 final size:10
Alignment explanation
Indices: 49918--49954 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
49908 TATTTTTTTC
49918 AAAAAAACAA
1 AAAAAAACAA
**
49928 AAAAAGGCAA
1 AAAAAAACAA
49938 AAAAAAACAA
1 AAAAAAACAA
49948 AAAAAAA
1 AAAAAAA
49955 ACCAAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.86, C:0.08, G:0.05, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:52552 original size:22 final size:24
Alignment explanation
Indices: 52506--52552 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
52496 TTAACCCAAC
52506 CTAATTCCTAATAAAATAATAAAT
1 CTAATTCCTAATAAAATAATAAAT
* *
52530 CTAA-TCCTAA-AAGATAATGAAT
1 CTAATTCCTAATAAAATAATAAAT
52552 C
1 C
52553 ATCATATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 11 0.52
23 6 0.29
24 4 0.19
ACGTcount: A:0.51, C:0.15, G:0.04, T:0.30
Consensus pattern (24 bp):
CTAATTCCTAATAAAATAATAAAT
Done.