Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000436.1 Hibiscus syriacus cultivar Beakdansim tig00000799_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: 35581
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:573 original size:21 final size:22
Alignment explanation
Indices: 549--590 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
539 TTGACGAATT
549 TTTGTAGA-AAGAG-AGAAATGC
1 TTTG-AGAGAAGAGAAGAAATGC
*
570 TTTGAGAGCAGAGAAGAAATG
1 TTTGAGAGAAGAGAAGAAATG
591 TTTTCTACGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 3 0.17
21 8 0.44
22 7 0.39
ACGTcount: A:0.43, C:0.05, G:0.31, T:0.21
Consensus pattern (22 bp):
TTTGAGAGAAGAGAAGAAATGC
Found at i:904 original size:21 final size:23
Alignment explanation
Indices: 871--918 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
861 CAATTGAGAG
871 AAAATATTCG-TTT-CACTTTGA
1 AAAATATTCGTTTTACACTTTGA
892 AAAATA-TCAGTTTTCACACTTTGA
1 AAAATATTC-GTTTT-ACACTTTGA
916 AAA
1 AAA
919 TGTGTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
20 2 0.09
21 7 0.30
22 3 0.13
24 11 0.48
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.38
Consensus pattern (23 bp):
AAAATATTCGTTTTACACTTTGA
Found at i:2558 original size:12 final size:13
Alignment explanation
Indices: 2541--2565 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2531 GGGAGATGTT
2541 AAAAAAGTAAAAA
1 AAAAAAGTAAAAA
2554 AAAAAAGTAAAA
1 AAAAAAGTAAAA
2566 GAATTTCATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (13 bp):
AAAAAAGTAAAAA
Found at i:8327 original size:44 final size:42
Alignment explanation
Indices: 8261--8363 Score: 140
Period size: 44 Copynumber: 2.5 Consensus size: 42
8251 ATAATAATTT
*
8261 AAAA-ATATATATAT-TATATAGTTTTGAAAATGATTTTTGA
1 AAAACATATATATATATATATAGTTTTGAAAATAATTTTTGA
* *
8301 ATATATATATATATATATATATTAGTTTTGAAAATAATTTTTGA
1 A-AAACATATATATATATATA-TAGTTTTGAAAATAATTTTTGA
8345 AAAACATATATAT-TATATA
1 AAAACATATATATATATATA
8364 GTTTTAATTT
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
40 1 0.02
41 2 0.04
42 16 0.29
43 14 0.25
44 22 0.40
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.46
Consensus pattern (42 bp):
AAAACATATATATATATATATAGTTTTGAAAATAATTTTTGA
Found at i:8431 original size:10 final size:10
Alignment explanation
Indices: 8416--8452 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
8406 AATATTAATT
8416 TTATTTTTTA
1 TTATTTTTTA
8426 TTATTTTTTA
1 TTATTTTTTA
*
8436 TTATTATTTA
1 TTATTTTTTA
8446 TTTATTT
1 -TTATTT
8453 ATTTTTCCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 19 0.79
11 5 0.21
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (10 bp):
TTATTTTTTA
Found at i:8441 original size:13 final size:13
Alignment explanation
Indices: 8419--8451 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
8409 ATTAATTTTA
8419 TTTT-TTATTATT
1 TTTTATTATTATT
8431 TTTTATTATTATT
1 TTTTATTATTATT
8444 TATTTATT
1 T-TTTATT
8452 TATTTTTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.21
13 9 0.47
14 6 0.32
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTATTATTATT
Found at i:9713 original size:22 final size:21
Alignment explanation
Indices: 9688--9728 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
9678 AAACTTTCTT
9688 TATTTTTTTATTTTTTATTTCA
1 TATTTTTTTA-TTTTTATTTCA
9710 TATTTTTTTATTTTTATTT
1 TATTTTTTTATTTTTATTT
9729 TTGCATTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.80
Consensus pattern (21 bp):
TATTTTTTTATTTTTATTTCA
Found at i:10551 original size:16 final size:16
Alignment explanation
Indices: 10530--10564 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
10520 TTGTATAACC
10530 AATTAAAATATATTTA
1 AATTAAAATATATTTA
* *
10546 AATTAAATTATGTTTA
1 AATTAAAATATATTTA
10562 AAT
1 AAT
10565 AGTTTTAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (16 bp):
AATTAAAATATATTTA
Found at i:11162 original size:6 final size:6
Alignment explanation
Indices: 11151--11193 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
11141 TCTACGATCT
11151 TCCTAA TCCTAA TCCTAA TCCTAA TCCTAA TCCTAA TCCTAA T
1 TCCTAA TCCTAA TCCTAA TCCTAA TCCTAA TCCTAA TCCTAA T
11194 TCATACCTGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.35
Consensus pattern (6 bp):
TCCTAA
Found at i:13454 original size:18 final size:18
Alignment explanation
Indices: 13422--13463 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
13412 AACATAGAAT
*
13422 ATAAATAAACCAACA-AA
1 ATAAATAAACAAACATAA
*
13439 GATAAATAAAGAAACATAA
1 -ATAAATAAACAAACATAA
13458 ATAAAT
1 ATAAAT
13464 TAACTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.69, C:0.10, G:0.05, T:0.17
Consensus pattern (18 bp):
ATAAATAAACAAACATAA
Found at i:14474 original size:2 final size:2
Alignment explanation
Indices: 14467--14500 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
14457 TCAATTTAAA
14467 AT AT 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 AT AT
14501 TTTACAAGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14686 original size:13 final size:13
Alignment explanation
Indices: 14657--14694 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
14647 ATGCAATCCA
14657 GGTGACATACG-G
1 GGTGACATACGAG
14669 GGTGACATACGAG
1 GGTGACATACGAG
14682 GGTGACATACGAG
1 GGTGACATACGAG
14695 CCATACGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.29, C:0.16, G:0.39, T:0.16
Consensus pattern (13 bp):
GGTGACATACGAG
Found at i:14798 original size:29 final size:29
Alignment explanation
Indices: 14748--14827 Score: 126
Period size: 29 Copynumber: 2.8 Consensus size: 29
14738 AGGAATAGAG
* *
14748 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTGT
14777 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
14806 AGGTCGCCATGTAGTCCCGGCG
1 AGGTCGCCATGTAGTCCCGGCG
14828 CCATTCCCAT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 46 0.96
30 2 0.04
ACGTcount: A:0.15, C:0.31, G:0.33, T:0.21
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:14932 original size:27 final size:27
Alignment explanation
Indices: 14900--14955 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
14890 CCTACAGCTC
14900 CCAATGCATGCATGTGAACCATTTGAG
1 CCAATGCATGCATGTGAACCATTTGAG
14927 CCAATGCATGCATGTGAACCATTTGAG
1 CCAATGCATGCATGTGAACCATTTGAG
14954 CC
1 CC
14956 GTGAATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (27 bp):
CCAATGCATGCATGTGAACCATTTGAG
Found at i:15137 original size:15 final size:17
Alignment explanation
Indices: 15117--15167 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 17
15107 GATTGCAGCC
15117 GAGAAAGAAA-AAAG-G
1 GAGAAAGAAAGAAAGAG
15132 GAGAAAGGAAAGAAAGAAAG
1 GAGAAA-GAAAGAAAG--AG
*
15152 GAGAAAGAAAGTAAGA
1 GAGAAAGAAAGAAAGA
15168 AGAAGAAAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
15 6 0.20
16 4 0.13
17 5 0.17
19 8 0.27
20 7 0.23
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (17 bp):
GAGAAAGAAAGAAAGAG
Found at i:15144 original size:20 final size:19
Alignment explanation
Indices: 15118--15168 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
15108 ATTGCAGCCG
15118 AGAAAGAAA-AAAGGGAGAA
1 AGAAAGAAAGAAA-GGAGAA
15137 AGGAAAGAAAGAAAGGAGAA
1 A-GAAAGAAAGAAAGGAGAA
*
15157 AGAAAGTAAGAA
1 AGAAAGAAAGAA
15169 GAAGAAAGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 11 0.38
20 15 0.52
21 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (19 bp):
AGAAAGAAAGAAAGGAGAA
Found at i:15171 original size:15 final size:15
Alignment explanation
Indices: 15118--15176 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 15
15108 ATTGCAGCCG
* **
15118 AGAAAGAAAAAAGGG
1 AGAAAGAAGAAAGAA
15133 AGAAAG--GAAAGAA
1 AGAAAGAAGAAAGAA
*
15146 AGAAAGGAGAAAGAA
1 AGAAAGAAGAAAGAA
*
15161 AGTAAGAAG-AAGAA
1 AGAAAGAAGAAAGAA
15175 AG
1 AG
15177 GGATATAAGG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
13 10 0.27
14 7 0.19
15 20 0.54
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (15 bp):
AGAAAGAAGAAAGAA
Found at i:15345 original size:41 final size:41
Alignment explanation
Indices: 15300--15388 Score: 92
Period size: 41 Copynumber: 2.2 Consensus size: 41
15290 TATATGATTG
* *
15300 TTAGTTTAAG-TT-ATAGTATACATAAATTAAAAATTATTTAA
1 TTAGTTTAAGTTTGATAGT-TACAT-AATTAAAAAATAATTAA
* * * *
15341 TTAGTATATGTTTGATAGTTATATAGTTAAAAAATAATTAA
1 TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
15382 TTAGTTT
1 TTAGTTT
15389 GTTTTGTTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 28 0.72
42 6 0.15
43 5 0.13
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (41 bp):
TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
Found at i:15401 original size:42 final size:39
Alignment explanation
Indices: 15325--15433 Score: 114
Period size: 41 Copynumber: 2.6 Consensus size: 39
15315 GTATACATAA
*
15325 ATTAAAAATTATTTAATTAGTATATG-TTTGATAGTTA-TAT
1 ATTAAAAAATATTTAATTAGT-T-TGTTTTGATAGTTAGT-T
*
15365 AGTTAAAAAATAATTAATTAGTTTGTTTTGTTATAGTTAGTT
1 A-TTAAAAAATATTTAATTAGTTTGTTTTG--ATAGTTAGTT
15407 ATATAAAAAATTATTTAATTAGTTTGT
1 AT-TAAAAAA-TATTTAATTAGTTTGT
15434 GTTAGTTAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
39 2 0.03
40 6 0.10
41 19 0.32
42 16 0.27
43 16 0.27
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (39 bp):
ATTAAAAAATATTTAATTAGTTTGTTTTGATAGTTAGTT
Found at i:15647 original size:16 final size:16
Alignment explanation
Indices: 15615--15661 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
15605 TTTAAAAAGT
*
15615 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
15631 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
15647 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
15662 AAGTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:15656 original size:15 final size:14
Alignment explanation
Indices: 15636--15666 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
15626 GTTTATTAGT
15636 TTATTATATTATAAG
1 TTATTATATTA-AAG
15651 TTATTATATTAAAG
1 TTATTATATTAAAG
15665 TT
1 TT
15667 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:16891 original size:21 final size:21
Alignment explanation
Indices: 16842--16891 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
16832 AATTTGTATT
16842 TTTTAATTATTATTTAAATTAA
1 TTTT-ATTATTATTTAAATTAA
* *
16864 CTATATTATTGATTTAAA-TAA
1 TTTTATTATT-ATTTAAATTAA
16885 TTTTATT
1 TTTTATT
16892 GTTTTTGTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTATTATTATTTAAATTAA
Found at i:17822 original size:17 final size:17
Alignment explanation
Indices: 17800--17832 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17790 CAATGATTTT
*
17800 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
17817 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
17833 AATATTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:17849 original size:24 final size:22
Alignment explanation
Indices: 17817--17885 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 22
17807 AAATCATTAC
17817 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
* *
17839 TAGTAAATCAACTATTTTAAATCA-T
1 TAGT--ATCAAATA-ATTAAAT-ATT
17864 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
17886 AACATAAATC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
21 1 0.03
22 11 0.29
23 7 0.18
24 7 0.18
25 11 0.29
26 1 0.03
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (22 bp):
TAGTATCAAATAATTAAATATT
Found at i:17913 original size:47 final size:46
Alignment explanation
Indices: 17817--17915 Score: 112
Period size: 47 Copynumber: 2.1 Consensus size: 46
17807 AAATCATTAC
* * * *
17817 TAGTATCAAATAATTAAATATTTAGTAAATCAACTATTTTAAATCAT
1 TAGTATCAAATAATTAAATATTAAATAAATC-ACTATTATAAATAAT
17864 TAGTATCAAATAATTAAATATTAACATAAATC-CTTATTA-ATAATAAT
1 TAGTATCAAATAATTAAATATTAA-ATAAATCAC-TATTATA-AATAAT
17911 TAGTA
1 TAGTA
17916 AATCATTAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
46 2 0.04
47 37 0.82
48 6 0.13
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.39
Consensus pattern (46 bp):
TAGTATCAAATAATTAAATATTAAATAAATCACTATTATAAATAAT
Found at i:18060 original size:14 final size:14
Alignment explanation
Indices: 18041--18080 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
18031 TAGTAATAAT
18041 TATTAAATCATTAG
1 TATTAAATCATTAG
*
18055 TATTAAATCATTAT
1 TATTAAATCATTAG
*
18069 TA-TAAATAATTA
1 TATTAAATCATTA
18081 CTAAATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (14 bp):
TATTAAATCATTAG
Found at i:18068 original size:38 final size:36
Alignment explanation
Indices: 18026--18141 Score: 110
Period size: 35 Copynumber: 3.1 Consensus size: 36
18016 GTATTCTATA
18026 ATTATTAGT-AATAATTATTAAATCATTAGTATTAAATC
1 ATTATTA-TAAATAATTATTAAAT-ATTA-TATTAAATC
* * * *
18064 ATTATTATAAATAATTACTAAATAATA-ACTAAATA
1 ATTATTATAAATAATTATTAAATATTATATTAAATC
* *
18099 ATTATTATAAATCATTATTATAATGATTATTATCAAATC
1 ATTATTATAAATAATTATTA-AAT-ATTA-TATTAAATC
18138 ATTA
1 ATTA
18142 CTAAATCATC
Statistics
Matches: 63, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
35 24 0.38
36 3 0.05
37 7 0.11
38 20 0.32
39 9 0.14
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (36 bp):
ATTATTATAAATAATTATTAAATATTATATTAAATC
Found at i:18129 original size:12 final size:13
Alignment explanation
Indices: 18039--18878 Score: 373
Period size: 12 Copynumber: 63.1 Consensus size: 13
18029 ATTAGTAATA
18039 ATTATTAAATCATT
1 ATTA-TAAATCATT
*
18053 AGTATTAAATCATT
1 ATTA-TAAATCATT
18067 ATTATAAAT-A--
1 ATTATAAATCATT
18077 ATTACTAAAT-A--
1 ATTA-TAAATCATT
* *
18088 ATAACTAAATAATT
1 ATTA-TAAATCATT
18102 ATTATAAATCATT
1 ATTATAAATCATT
*
18115 ATTAT-AATGATT
1 ATTATAAATCATT
18127 ATTATCAAATCATT
1 ATTAT-AAATCATT
18141 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
18160 AAATT-TAAATCATT
1 --ATTATAAATCATT
18174 A-T-TAAATCATT
1 ATTATAAATCATT
* *
18185 TTTAT-AATGATT
1 ATTATAAATCATT
*
18197 ATTGCTAAATCATT
1 ATT-ATAAATCATT
*
18211 ATTAT-AATGATT
1 ATTATAAATCATT
18223 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
18237 ACTAT-AATGATT
1 ATTATAAATCATT
18249 ATTATCAAATCATT
1 ATTAT-AAATCATT
18263 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
*
18282 AAATATTTAAATCATT
1 --AT-TATAAATCATT
18298 A-T-TAAATCATT
1 ATTATAAATCATT
* *
18309 TTTAT-AATGATT
1 ATTATAAATCATT
18321 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
18335 ATTAT-AATGATT
1 ATTATAAATCATT
18347 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
18361 ACTAT-AATGATT
1 ATTATAAATCATT
18373 ATTATCAAATCATT
1 ATTAT-AAATCATT
18387 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
*
18406 AAATATTTAAATCATT
1 --AT-TATAAATCATT
18422 A-T-TAAATCATT
1 ATTATAAATCATT
*
18433 -TT-T-AATGATT
1 ATTATAAATCATT
18443 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
18457 ATTAT-AATGATT
1 ATTATAAATCATT
18469 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
18483 ACTAT-AATGATT
1 ATTATAAATCATT
18495 ATTATCAAATCATT
1 ATTAT-AAATCATT
18509 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
* ** * *
18528 A-AATATTTAATC
1 ATTATAAATCATT
18540 ATTATAAATCATT
1 ATTATAAATCATT
* *
18553 TTTAT-AATGATT
1 ATTATAAATCATT
18565 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
18579 ATTAT-AATGATT
1 ATTATAAATCATT
18591 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
18605 ACTAT-AATGATT
1 ATTATAAATCATT
18617 ATTATCAAATCATT
1 ATTAT-AAATCATT
*
18631 A--CTAAATCATT
1 ATTATAAATCATT
* * * * *
18642 A-AATCATTAAAT
1 ATTATAAATCATT
18654 ATT-TAAATCATT
1 ATTATAAATCATT
18666 A-T-TAAATCATT
1 ATTATAAATCATT
* *
18677 TTTAT-AATGATT
1 ATTATAAATCATT
18689 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
18703 ATTAT-AATGATT
1 ATTATAAATCATT
18715 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
18729 ACTAT-AATGATT
1 ATTATAAATCATT
18741 ATTATCAAATCATT
1 ATTAT-AAATCATT
18755 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
*
18774 AAATATTTAAATCATT
1 --AT-TATAAATCATT
18790 A-T-TAAATCATT
1 ATTATAAATCATT
*
18801 -TTAT-AATGATT
1 ATTATAAATCATT
18812 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
18826 ATTAT-AATGATT
1 ATTATAAATCATT
18838 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
18852 ACTAT-AATGATT
1 ATTATAAATCATT
18864 ATTATCAAATCATT
1 ATTAT-AAATCATT
18878 A
1 A
18879 CTAAATCATC
Statistics
Matches: 647, Mismatches: 89, Indels: 180
0.71 0.10 0.20
Matches are distributed among these distances:
10 10 0.02
11 82 0.13
12 203 0.31
13 45 0.07
14 198 0.31
15 6 0.01
16 24 0.04
17 4 0.01
18 11 0.02
19 56 0.09
20 4 0.01
21 4 0.01
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.43
Consensus pattern (13 bp):
ATTATAAATCATT
Found at i:18137 original size:26 final size:26
Alignment explanation
Indices: 18039--18878 Score: 608
Period size: 26 Copynumber: 34.2 Consensus size: 26
18029 ATTAGTAATA
* * *
18039 ATTATTA-AATCATTAGTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
* *
18064 ATTATTATAA--ATAATTA-CTAAATA
1 ATTATTATAATGATTATTATC-AAATC
* * *
18088 ATAACTA-AATAATTATTAT-AAATC
1 ATTATTATAATGATTATTATCAAATC
18112 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* *
18138 ATTA--CT-A--A--ATCATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* *
18157 ATTAAATT-TAA--ATCATTATTAAATC
1 ATT--ATTATAATGATTATTATCAAATC
* *
18182 ATTTTTATAATGATTATT-GCTAAATC
1 ATTATTATAATGATTATTATC-AAATC
18208 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
*
18234 ATTACTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* * * * * *
18260 ATTACTA-AATCATCA-AATC-ATTA
1 ATTATTATAATGATTATTATCAAATC
* * *
18283 AATATT-TAA--ATCATTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
*
18306 ATTTTTATAATGATTATTA-CTAAATC
1 ATTATTATAATGATTATTATC-AAATC
18332 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
*
18358 ATTACTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* * * * * *
18384 ATTACTA-AATCATCA-AATC-ATTA
1 ATTATTATAATGATTATTATCAAATC
* * *
18407 AATATT-TAA--ATCATTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
18430 ATT-TT-TAATGATTATTA-CTAAATC
1 ATTATTATAATGATTATTATC-AAATC
18454 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
*
18480 ATTACTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* *
18506 ATTA--CT-A--A--ATCATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* * * *
18525 ATTA-AATATTTAATCATTAT-AAATC
1 ATTATTATA-ATGATTATTATCAAATC
*
18550 ATTTTTATAATGATTATTA-CTAAATC
1 ATTATTATAATGATTATTATC-AAATC
18576 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
*
18602 ATTACTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* * * * *
18628 ATTACTA-AATCATTA-AATC-ATTA
1 ATTATTATAATGATTATTATCAAATC
* * *
18651 AATATT-TAA--ATCATTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
*
18674 ATTTTTATAATGATTATTA-CTAAATC
1 ATTATTATAATGATTATTATC-AAATC
18700 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
*
18726 ATTACTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* * * * * *
18752 ATTACTA-AATCATCA-AATC-ATTA
1 ATTATTATAATGATTATTATCAAATC
* * *
18775 AATATT-TAA--ATCATTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
18798 ATT-TTATAATGATTATTA-CTAAATC
1 ATTATTATAATGATTATTATC-AAATC
18823 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
*
18849 ATTACTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
18875 ATTA
1 ATTA
18879 CTAAATCATC
Statistics
Matches: 653, Mismatches: 98, Indels: 127
0.74 0.11 0.14
Matches are distributed among these distances:
19 27 0.04
20 1 0.00
21 18 0.03
22 16 0.02
23 63 0.10
24 61 0.09
25 92 0.14
26 369 0.57
27 6 0.01
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.43
Consensus pattern (26 bp):
ATTATTATAATGATTATTATCAAATC
Found at i:18332 original size:124 final size:124
Alignment explanation
Indices: 18055--18936 Score: 1606
Period size: 124 Copynumber: 7.2 Consensus size: 124
18045 AAATCATTAG
* * * * * *
18055 TATTAAATCATTATTATAA--ATAATTACTAAATAATAACTA-AATAATTATTAT-AAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
*
18116 TTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATT-AA-ATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
*
18173 TATTAAATCATTTTTATAATGATTATTGCTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
18238 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
18297 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
18362 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
18421 TATTAAATCA-TTTT-TAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
18484 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTT-AATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
18542 TA-TAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
*
18606 CTATAATGATTATTATCAAATCATTACTAAATCATTAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
18665 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
18730 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
18789 TATTAAATCA-TTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
18853 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
18912 TATTAAATCATTTTTATAATGATTA
1 TATTAAATCATTTTTATAATGATTA
18937 ATAAATACAT
Statistics
Matches: 742, Mismatches: 11, Indels: 16
0.96 0.01 0.02
Matches are distributed among these distances:
118 18 0.02
120 23 0.03
121 23 0.03
122 253 0.34
123 137 0.18
124 288 0.39
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.43
Consensus pattern (124 bp):
TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
Found at i:18506 original size:368 final size:369
Alignment explanation
Indices: 18055--18936 Score: 1605
Period size: 368 Copynumber: 2.4 Consensus size: 369
18045 AAATCATTAG
* * * * *
18055 TATTAAATCATTATTATAA--ATAATTACTAAATAATAACTA-AATAATTATTAT-AAATCATTA
1 TATTAAATCATT-TTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
*
18116 TTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATTTAAATCATTATTAAAT
65 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATTTAAATCATTATTAAAT
*
18181 CATTTTTATAATGATTATTGCTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATG
130 CATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATG
18246 ATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTT
195 ATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTT
18311 TATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATT
260 TATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATT
18376 ATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
325 ATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
18421 TATTAAATCATTTT-TAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTAC
1 TATTAAATCATTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTAC
*
18485 TATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAATCATTA-TAAAT
66 TATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAAT-TTAAATCATTATTAAAT
18549 CATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATG
130 CATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATG
*
18614 ATTATTATCAAATCATTACTAAATCATTAAATCATTAAATATTTAAATCATTATTAAATCATTTT
195 ATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTT
18679 TATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATT
260 TATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATT
18744 ATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
325 ATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
18789 TATTAAATCATTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTAC
1 TATTAAATCATTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTAC
18854 TATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAA
66 TATAATGATTATTATCAAATCATTACTAAATCATCAAATCATT-AA-ATTTAAATCATTATTAAA
18919 TCATTTTTATAATGATTA
129 TCATTTTTATAATGATTA
18937 ATAAATACAT
Statistics
Matches: 497, Mismatches: 10, Indels: 13
0.96 0.02 0.03
Matches are distributed among these distances:
364 3 0.01
365 2 0.00
366 29 0.06
367 11 0.02
368 313 0.63
369 103 0.21
370 12 0.02
371 24 0.05
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.43
Consensus pattern (369 bp):
TATTAAATCATTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTAC
TATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATTTAAATCATTATTAAATC
ATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGA
TTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTT
ATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTA
TCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
Found at i:18646 original size:8 final size:8
Alignment explanation
Indices: 18633--18666 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
18623 AAATCATTAC
18633 TAAATCAT
1 TAAATCAT
18641 TAAATCAT
1 TAAATCAT
18649 TAAAT-ATT
1 TAAATCA-T
18657 TAAATCAT
1 TAAATCAT
18665 TA
1 TA
18667 TTAAATCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 1 0.04
8 22 0.92
9 1 0.04
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (8 bp):
TAAATCAT
Found at i:21998 original size:26 final size:24
Alignment explanation
Indices: 21940--21998 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
21930 CTAATAAACC
*
21940 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
21964 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
21992 TAATAAT
1 TAATAAT
21999 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:22069 original size:19 final size:20
Alignment explanation
Indices: 22042--22085 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
22032 TATAAATATT
*
22042 TAATGATTTAG-ATTAATAC
1 TAATCATTTAGAATTAATAC
*
22061 TAATCATTTAGTAATTATTAC
1 TAATCATTTAG-AATTAATAC
22082 TAAT
1 TAAT
22086 AATAATGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
21 11 0.52
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (20 bp):
TAATCATTTAGAATTAATAC
Found at i:22280 original size:16 final size:16
Alignment explanation
Indices: 22259--22314 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 16
22249 AATGTAAATT
22259 AAACAAAATATTTTTA
1 AAACAAAATATTTTTA
22275 AAACAACACTAATATTTTT-
1 AAAC-A-A--AATATTTTTA
*
22294 AAACACAATATTTTTTA
1 AAACAAAATA-TTTTTA
22311 AAAC
1 AAAC
22315 GGAAATTATC
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
15 4 0.12
16 9 0.27
17 5 0.15
18 2 0.06
19 4 0.12
20 9 0.27
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (16 bp):
AAACAAAATATTTTTA
Found at i:22305 original size:15 final size:16
Alignment explanation
Indices: 22279--22308 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
22269 TTTTTAAAAC
22279 AACACTAATATTTTTA
1 AACACTAATATTTTTA
22295 AACAC-AATATTTTT
1 AACACTAATATTTTT
22309 TAAAACGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.43
Consensus pattern (16 bp):
AACACTAATATTTTTA
Found at i:22814 original size:45 final size:45
Alignment explanation
Indices: 22720--22814 Score: 124
Period size: 45 Copynumber: 2.1 Consensus size: 45
22710 TTAAAGACAC
* * *
22720 TAACAAATTAATTAATATTTTTTATATTTAATAACTTAAACTAGA
1 TAACTAATTAACTAATATTTTTTATATATAATAACTTAAACTAGA
22765 -AACTAATTAACTAAT-TTTTTTATATAATATATAACTTAAACTA-A
1 TAACTAATTAACTAATATTTTTTATAT-ATA-ATAACTTAAACTAGA
22809 TAACTA
1 TAACTA
22815 TATAATATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
43 10 0.23
44 16 0.36
45 18 0.41
ACGTcount: A:0.47, C:0.08, G:0.01, T:0.43
Consensus pattern (45 bp):
TAACTAATTAACTAATATTTTTTATATATAATAACTTAAACTAGA
Found at i:22819 original size:28 final size:29
Alignment explanation
Indices: 22785--22851 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 29
22775 CTAATTTTTT
*
22785 TATATAATATATAACTTAAACTAA-TAAC
1 TATATAATATATAACTTAAACTAACAAAC
22813 TATAT-A-ATATAACTTAAACTAACAAAC
1 TATATAATATATAACTTAAACTAACAAAC
*
22840 TA-ATAATTTATA
1 TATATAATATATA
22852 CTAACAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
26 18 0.53
27 7 0.21
28 9 0.26
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (29 bp):
TATATAATATATAACTTAAACTAACAAAC
Found at i:22854 original size:21 final size:21
Alignment explanation
Indices: 22821--22869 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
22811 ACTATATAAT
22821 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
22842 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
22863 ATTAACT
1 A-TAACT
22870 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:23487 original size:81 final size:81
Alignment explanation
Indices: 23397--23560 Score: 328
Period size: 81 Copynumber: 2.0 Consensus size: 81
23387 ACAGCATGCA
23397 TCCCCTCCCCCATGCATTCCCACGTCCCATGTTGATTGCATGGCGACCTATTCCTTTGCAAAATA
1 TCCCCTCCCCCATGCATTCCCACGTCCCATGTTGATTGCATGGCGACCTATTCCTTTGCAAAATA
23462 CACACAGGTCGGTCGC
66 CACACAGGTCGGTCGC
23478 TCCCCTCCCCCATGCATTCCCACGTCCCATGTTGATTGCATGGCGACCTATTCCTTTGCAAAATA
1 TCCCCTCCCCCATGCATTCCCACGTCCCATGTTGATTGCATGGCGACCTATTCCTTTGCAAAATA
23543 CACACAGGTCGGTCGC
66 CACACAGGTCGGTCGC
23559 TC
1 TC
23561 GGATGCCATG
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.20, C:0.37, G:0.17, T:0.26
Consensus pattern (81 bp):
TCCCCTCCCCCATGCATTCCCACGTCCCATGTTGATTGCATGGCGACCTATTCCTTTGCAAAATA
CACACAGGTCGGTCGC
Found at i:23598 original size:29 final size:29
Alignment explanation
Indices: 23553--23612 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
23543 CACACAGGTC
* *
23553 GGTCGCTCGGATGCCATGGCGACCTCCAA
1 GGTCGCCCGGATACCATGGCGACCTCCAA
23582 GGTCGCCCGGATACCATGGCGACCTCCAA
1 GGTCGCCCGGATACCATGGCGACCTCCAA
23611 GG
1 GG
23613 CCACTGTAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.18, C:0.35, G:0.32, T:0.15
Consensus pattern (29 bp):
GGTCGCCCGGATACCATGGCGACCTCCAA
Found at i:24058 original size:8 final size:8
Alignment explanation
Indices: 24045--24085 Score: 75
Period size: 8 Copynumber: 5.2 Consensus size: 8
24035 GGGACACGTA
24045 TTATAATT
1 TTATAATT
24053 TTATAATT
1 TTATAATT
24061 TTATAATT
1 TTATAATT
24069 TTATAATT
1 TTATAATT
24077 TTA-AATT
1 TTATAATT
24084 TT
1 TT
24086 TTATTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 6 0.18
8 27 0.82
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TTATAATT
Found at i:24286 original size:22 final size:22
Alignment explanation
Indices: 24243--24294 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
24233 TATCACTATC
* **
24243 GAATTTAAAGGATTGAGTATTT
1 GAATTTAGAGGATTGAAAATTT
24265 GGAATTTAGA-GATTGAAAATTT
1 -GAATTTAGAGGATTGAAAATTT
*
24287 AAATTTAG
1 GAATTTAG
24295 GTATTTGAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 7 0.28
22 10 0.40
23 8 0.32
ACGTcount: A:0.40, C:0.00, G:0.21, T:0.38
Consensus pattern (22 bp):
GAATTTAGAGGATTGAAAATTT
Found at i:24443 original size:2 final size:2
Alignment explanation
Indices: 24436--24473 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
24426 GATTGAAGTG
24436 AT AT AT AT 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 AT AT AT AT
24474 TTAAAAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.