Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006668.1 Hibiscus syriacus cultivar Beakdansim tig00016516_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: 77239
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3089 original size:3 final size:3
Alignment explanation
Indices: 3071--3131 Score: 99
Period size: 3 Copynumber: 21.0 Consensus size: 3
3061 TTTTGCCCAT
3071 TTA TT- TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
3117 TGA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
3132 AATAAATATT
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
2 4 0.07
3 50 0.93
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4266 original size:2 final size:2
Alignment explanation
Indices: 4259--4348 Score: 180
Period size: 2 Copynumber: 45.0 Consensus size: 2
4249 TTAGTCACCG
4259 TA TA TA 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
4301 TA TA TA 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
4343 TA TA TA
1 TA TA TA
4349 GAGGGTAAAT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 88 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6055 original size:19 final size:18
Alignment explanation
Indices: 6022--6082 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 18
6012 ATTATTATTT
*
6022 ATATTAATATATTTATGTAA
1 ATATT-ATATTTTTAT-TAA
6042 ATATTATATTTTTATTAA
1 ATATTATATTTTTATTAA
* *
6060 A-ATAATATTTATA-TAA
1 ATATTATATTTTTATTAA
*
6076 TTATTAT
1 ATATTAT
6083 TTATTTAGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 3 0.09
17 14 0.40
18 4 0.11
19 9 0.26
20 5 0.14
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
ATATTATATTTTTATTAA
Found at i:6088 original size:36 final size:32
Alignment explanation
Indices: 6001--6089 Score: 90
Period size: 34 Copynumber: 2.7 Consensus size: 32
5991 GTTAGTATTT
* *
6001 TTTAAATAGTTATTATTATTTATATTAATATA
1 TTTATATAATTATTATTATTTATATTAATATA
* * *
6033 TTTATGTAAATATTA-TATTTTTATTAAAATAATA
1 TTTATATAATTATTATTATTTATATT--AAT-ATA
6067 TTTATATAATTATTATTTATTTA
1 TTTATATAATTATTA-TTATTTA
6090 GAATTATTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
31 9 0.20
32 11 0.25
33 3 0.07
34 16 0.36
36 5 0.11
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (32 bp):
TTTATATAATTATTATTATTTATATTAATATA
Found at i:6248 original size:17 final size:17
Alignment explanation
Indices: 6226--6279 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
6216 AATGTTAATA
6226 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
6243 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
6260 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
6277 TTT
1 TTT
6280 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:7886 original size:21 final size:21
Alignment explanation
Indices: 7860--7932 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
7850 TATGCCATCT
*
7860 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
7881 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
7902 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
7923 CCGCAGGGTT
1 CCGCAGGGTT
7933 TTATACCATA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.04
21 44 0.92
22 2 0.04
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:8514 original size:33 final size:34
Alignment explanation
Indices: 8455--8551 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
8445 AAATGTTTTT
*
8455 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
8489 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
8522 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
8552 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:8558 original size:34 final size:33
Alignment explanation
Indices: 8453--8558 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
8443 ATAAATGTTT
*
8453 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
8487 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
8519 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
8554 TTAAA
1 TTAAA
8559 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:9258 original size:127 final size:128
Alignment explanation
Indices: 8952--9559 Score: 880
Period size: 127 Copynumber: 4.9 Consensus size: 128
8942 TTACCTGATT
8952 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
* **
9017 TGACAAAATAATGGAAGGCGTGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-CAATAGAGAAATAATAGG
9080 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
**
9145 TGACAAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-CAATAGAGAAATAATAGG
*
9207 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGACAATG-------A---TA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
* *
9262 --AC---AT-ATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCAATAGAGAAATAATAGG
* *
9319 TACTGATATATCTAGTGT-CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTATC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
** * * *
9383 TGATGAAATAATGGAAGGCGCGCCCCCAGGAACGCGCCTT-ATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCAATAGAGAAATAATAGG
* *
9445 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGATATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
* *
9510 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATA
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCAATA
9560 ATACTCCGAT
Statistics
Matches: 446, Mismatches: 14, Indels: 40
0.89 0.03 0.08
Matches are distributed among these distances:
111 45 0.10
112 54 0.12
115 2 0.00
117 2 0.00
118 1 0.00
120 1 0.00
121 1 0.00
123 1 0.00
126 42 0.09
127 202 0.45
128 95 0.21
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCAATAGAGAAATAATAGG
Found at i:9369 original size:111 final size:111
Alignment explanation
Indices: 9155--9378 Score: 371
Period size: 111 Copynumber: 2.0 Consensus size: 111
9145 TGACAAAATA
**
9155 ATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGGTACTGATATATCT
1 ATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTCCAATGAGAAATAATAGGTACTGATATATCT
9220 AGTGTCCCCGAGGGACATGAGTGACATAATAGGACAATGATAACAT
66 AGTGTCCCCGAGGGACATGAGTGACATAATAGGACAATGATAACAT
* *
9266 ATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGGTACTGATATAT
1 ATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTCCAAT-GAGAAATAATAGGTACTGATATAT
*
9330 CTAGTGT-CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACAT
64 CTAGTGTCCCCGAGGGACATGAGTGACATAATAGGACAATGATAACAT
9377 AT
1 AT
9379 TATCTGATGA
Statistics
Matches: 106, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
111 54 0.51
112 52 0.49
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (111 bp):
ATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTCCAATGAGAAATAATAGGTACTGATATATCT
AGTGTCCCCGAGGGACATGAGTGACATAATAGGACAATGATAACAT
Found at i:9447 original size:238 final size:239
Alignment explanation
Indices: 9027--9505 Score: 759
Period size: 238 Copynumber: 2.0 Consensus size: 239
9017 TGACAAAATA
* **
9027 ATGGAAGGCGTGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGGTACTGATATATC
1 ATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCAATGAGAAATAATAGGTACTGATATATC
*
9092 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTATGACAAAATAAT
66 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTATATGACAAAATAAT
* **
9157 GGAAGGCGCGCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGGTACTGATATATCTAG
131 GGAAGGCGCGCCCCAGGAACGCGCCTTCATGTCCAATGAGAAATAATAGGTACTGATATATCTAG
9222 TGTCCCCGAGGGACATGAGTGACATAATAGGACAATGATAACAT
196 TGTCCCCGAGGGACATGAGTGACATAATAGGACAATGATAACAT
* *
9266 ATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGGTACTGATATAT
1 ATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCAAT-GAGAAATAATAGGTACTGATATAT
* **
9330 CTAGTGT-CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTATCTGATGAAATAA
65 CTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTATATGACAAAATAA
* *
9394 TGGAAGGCGCGCCCCCAGGAACGCGCCTT-ATGT-GAATAGTGAAATAATAGGTACTGATATATC
130 TGGAAGGCGCG-CCCCAGGAACGCGCCTTCATGTCCAAT-GAGAAATAATAGGTACTGATATATC
* *
9457 TAGTGTCCCCGAGGGACATGAGTGATATAATAGGGCAATGATAACAT
193 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGACAATGATAACAT
9504 AT
1 AT
9506 TCTCTGACGA
Statistics
Matches: 221, Mismatches: 16, Indels: 7
0.91 0.07 0.03
Matches are distributed among these distances:
237 1 0.00
238 140 0.63
239 80 0.36
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.23
Consensus pattern (239 bp):
ATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCAATGAGAAATAATAGGTACTGATATATC
TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTATATGACAAAATAAT
GGAAGGCGCGCCCCAGGAACGCGCCTTCATGTCCAATGAGAAATAATAGGTACTGATATATCTAG
TGTCCCCGAGGGACATGAGTGACATAATAGGACAATGATAACAT
Found at i:9645 original size:8 final size:8
Alignment explanation
Indices: 9632--9672 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
9622 TCACAATCTT
9632 TCAAATTC
1 TCAAATTC
9640 TCAAATTC
1 TCAAATTC
* *
9648 CCAAACTC
1 TCAAATTC
9656 T-AAATTC
1 TCAAATTC
9663 TCAAATTC
1 TCAAATTC
9671 TC
1 TC
9673 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:21347 original size:22 final size:22
Alignment explanation
Indices: 21315--21359 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
21305 TATATCTTAT
*
21315 GATTAAGCCTAATCTAGGTAAG
1 GATTAAACCTAATCTAGGTAAG
*
21337 GATTAAACCTAATTTAGGTAAG
1 GATTAAACCTAATCTAGGTAAG
21359 G
1 G
21360 CTATATACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (22 bp):
GATTAAACCTAATCTAGGTAAG
Found at i:22116 original size:41 final size:41
Alignment explanation
Indices: 22054--22139 Score: 136
Period size: 41 Copynumber: 2.1 Consensus size: 41
22044 TATGAATGCT
* *
22054 TATATTCTGTTTTGTAATTGCATTTTTATATCAAACAGAAA
1 TATAATCTGTTTTGTAATTGCATTTGTATATCAAACAGAAA
* *
22095 TATAATCTGTTTTGTAATTGCATTTGTATATCGAACATAAA
1 TATAATCTGTTTTGTAATTGCATTTGTATATCAAACAGAAA
22136 TATA
1 TATA
22140 TTTATTTATG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.35, C:0.09, G:0.10, T:0.45
Consensus pattern (41 bp):
TATAATCTGTTTTGTAATTGCATTTGTATATCAAACAGAAA
Found at i:22952 original size:15 final size:16
Alignment explanation
Indices: 22931--22979 Score: 73
Period size: 15 Copynumber: 3.1 Consensus size: 16
22921 GAGTATTTAA
22931 AATTATTTTATATTTT
1 AATTATTTTATATTTT
*
22947 AA-TATTTTATATATT
1 AATTATTTTATATTTT
22962 AATTATTTTATAATTTT
1 AATTATTTTAT-ATTTT
22979 A
1 A
22980 TGAGATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 14 0.48
16 10 0.34
17 5 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
AATTATTTTATATTTT
Found at i:26202 original size:33 final size:33
Alignment explanation
Indices: 26160--26234 Score: 105
Period size: 33 Copynumber: 2.3 Consensus size: 33
26150 ATTTTTCATT
** *
26160 TTATTATTATTATAATTATTTTTATAAATATTA
1 TTATTATTATTATAATTATTACTATAAATAATA
*
26193 TTATTATTATTATTATTATTACTATAAATAATA
1 TTATTATTATTATAATTATTACTATAAATAATA
*
26226 ATATTATTA
1 TTATTATTA
26235 CAGGCCAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (33 bp):
TTATTATTATTATAATTATTACTATAAATAATA
Found at i:26233 original size:3 final size:3
Alignment explanation
Indices: 26160--26213 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
26150 ATTTTTCATT
* * * *
26160 TTA TTA TTA TTA TAA TTA TTT TTA TAA ATA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
26208 TTA TTA
1 TTA TTA
26214 CTATAAATAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:26382 original size:23 final size:23
Alignment explanation
Indices: 26352--26396 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
26342 TCTTCTCTGC
26352 CGCCTCTACTCCAACTGCTCCGT
1 CGCCTCTACTCCAACTGCTCCGT
26375 CGCCTCTACTCCAACTGCTCCG
1 CGCCTCTACTCCAACTGCTCCG
26397 CCGTCATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.13, C:0.49, G:0.13, T:0.24
Consensus pattern (23 bp):
CGCCTCTACTCCAACTGCTCCGT
Found at i:26842 original size:22 final size:22
Alignment explanation
Indices: 26814--26863 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
26804 GAATAGTGAC
*
26814 CGGTGGTC-GAAATAGTGATCGG
1 CGGTGGTCAG-AATAGTAATCGG
26836 CGGTGGTCAGAATAGTAATCGG
1 CGGTGGTCAGAATAGTAATCGG
26858 CGGTGG
1 CGGTGG
26864 CCGACCGGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 25 0.96
23 1 0.04
ACGTcount: A:0.22, C:0.14, G:0.42, T:0.22
Consensus pattern (22 bp):
CGGTGGTCAGAATAGTAATCGG
Found at i:28387 original size:26 final size:27
Alignment explanation
Indices: 28335--28392 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
28325 TAATTCTTTC
*
28335 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATAC-TATTA
* *
28363 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCAAAATATTTATATATACTATTA
28389 TTTT
1 TTTT
28393 TTATTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
28 18 0.67
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATACTATTA
Found at i:28394 original size:28 final size:28
Alignment explanation
Indices: 28335--28394 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 28
28325 TAATTCTTTC
*
28335 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATTTATATATATACTTATTA
*
28363 TTTTCATAATATTTATATGTATA-TTATT-
1 TTTTCA-AA-ATTTATATATATACTTATTA
28391 TTTT
1 TTTT
28395 ATTTTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 10 0.36
29 7 0.25
30 11 0.39
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.62
Consensus pattern (28 bp):
TTTTCAAAATTTATATATATACTTATTA
Found at i:32861 original size:16 final size:16
Alignment explanation
Indices: 32833--32880 Score: 71
Period size: 16 Copynumber: 2.9 Consensus size: 16
32823 CTTGAAGAAG
32833 AGAAAAAAGGAAAAAAA
1 AGAAAAAA-GAAAAAAA
32850 AGAAAAAAGAAAAAAA
1 AGAAAAAAGAAAAAAA
32866 AGAAGAAAA-AAAAAA
1 AGAA-AAAAGAAAAAA
32881 TTGAATCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
16 18 0.60
17 12 0.40
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (16 bp):
AGAAAAAAGAAAAAAA
Found at i:33397 original size:32 final size:32
Alignment explanation
Indices: 33334--33400 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
33324 AGAGTCTGGA
* * * *
33334 AACAAGAAGTATTTATACGAGATGAGCATAAC
1 AACAAGAAATATCTATACCAGATAAGCATAAC
* *
33366 AACAAGAAATATCTCTACCAGATAAGTATAAC
1 AACAAGAAATATCTATACCAGATAAGCATAAC
33398 AAC
1 AAC
33401 CATTTCTTCA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.21
Consensus pattern (32 bp):
AACAAGAAATATCTATACCAGATAAGCATAAC
Found at i:34704 original size:19 final size:19
Alignment explanation
Indices: 34677--34715 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
34667 GGCTGCTGGA
34677 AACCAGTTTAACCGGTCTG
1 AACCAGTTTAACCGGTCTG
* *
34696 AACCGGTTTTACCGGTCTG
1 AACCAGTTTAACCGGTCTG
34715 A
1 A
34716 CCCAACCCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (19 bp):
AACCAGTTTAACCGGTCTG
Found at i:34737 original size:12 final size:11
Alignment explanation
Indices: 34720--34778 Score: 50
Period size: 12 Copynumber: 5.3 Consensus size: 11
34710 GTCTGACCCA
34720 ACCCGACTGTTG
1 ACCCGAC-GTTG
*
34732 ACCCGAC-CTG
1 ACCCGACGTTG
34742 ACCCGACCGTTG
1 ACCCGA-CGTTG
**
34754 ACCCGAC-CCG
1 ACCCGACGTTG
34764 ACCCGACCGTTG
1 ACCCGA-CGTTG
34776 ACC
1 ACC
34779 GTTGACTTTC
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
10 15 0.41
11 3 0.08
12 19 0.51
ACGTcount: A:0.19, C:0.46, G:0.22, T:0.14
Consensus pattern (11 bp):
ACCCGACGTTG
Found at i:34739 original size:22 final size:22
Alignment explanation
Indices: 34714--34778 Score: 103
Period size: 22 Copynumber: 3.0 Consensus size: 22
34704 TTACCGGTCT
* *
34714 GACCCAACCCGACTGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
34736 GACCTGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
34758 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
34779 GTTGACTTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.20, C:0.46, G:0.22, T:0.12
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:34745 original size:10 final size:10
Alignment explanation
Indices: 34730--34771 Score: 57
Period size: 10 Copynumber: 4.0 Consensus size: 10
34720 ACCCGACTGT
34730 TGACCCGACC
1 TGACCCGACC
34740 TGACCCGACC
1 TGACCCGACC
34750 GTTGACCCGACC
1 --TGACCCGACC
*
34762 CGACCCGACC
1 TGACCCGACC
34772 GTTGACCGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 19 0.66
12 10 0.34
ACGTcount: A:0.19, C:0.50, G:0.21, T:0.10
Consensus pattern (10 bp):
TGACCCGACC
Found at i:41964 original size:9 final size:9
Alignment explanation
Indices: 41950--42043 Score: 80
Period size: 9 Copynumber: 9.8 Consensus size: 9
41940 GGCTACTGGA
41950 AACCGGTTT
1 AACCGGTTT
41959 AACCGGTTTTT
1 AACCGG--TTT
41970 AACCGGTTT
1 AACCGGTTT
*
41979 GACCGGTTT
1 AACCGGTTT
*
41988 CAACCGGTTCG
1 -AACCGGTT-T
41999 AACCGGTTT
1 AACCGGTTT
* *
42008 GACCGGTCTG
1 AACCGGT-TT
42018 AACCGGTTT
1 AACCGGTTT
* *
42027 GACCGGTCTG
1 AACCGGT-TT
42037 AACCGGT
1 AACCGGT
42044 CTGACCCGAC
Statistics
Matches: 68, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
9 30 0.44
10 29 0.43
11 9 0.13
ACGTcount: A:0.18, C:0.26, G:0.28, T:0.29
Consensus pattern (9 bp):
AACCGGTTT
Found at i:41994 original size:19 final size:19
Alignment explanation
Indices: 41950--42043 Score: 102
Period size: 19 Copynumber: 4.9 Consensus size: 19
41940 GGCTACTGGA
41950 AACCGGTTT-AACCGGTTTTT
1 AACCGGTTTGAACCGG--TTT
41970 AACCGGTTTG-ACCGGTTT
1 AACCGGTTTGAACCGGTTT
*
41988 CAACCGGTTCGAACCGGTTT
1 -AACCGGTTTGAACCGGTTT
* *
42008 GACCGGTCTGAACCGGTTT
1 AACCGGTTTGAACCGGTTT
* *
42027 GACCGGTCTGAACCGGT
1 AACCGGTTTGAACCGGT
42044 CTGACCCGAC
Statistics
Matches: 67, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
18 3 0.04
19 42 0.63
20 22 0.33
ACGTcount: A:0.18, C:0.26, G:0.28, T:0.29
Consensus pattern (19 bp):
AACCGGTTTGAACCGGTTT
Found at i:42002 original size:29 final size:28
Alignment explanation
Indices: 41951--42043 Score: 107
Period size: 29 Copynumber: 3.2 Consensus size: 28
41941 GCTACTGGAA
*
41951 ACCGGTTTAACCGGTTTTTAACCGGTTTG
1 ACCGGTTTAACCGG-TTTGAACCGGTTTG
*
41980 ACCGGTTTCAACCGGTTCGAACCGGTTTG
1 ACCGGTTT-AACCGGTTTGAACCGGTTTG
* *
42009 ACCGGTCTGAACCGGTTTG-ACCGGTCTG
1 ACCGGT-TTAACCGGTTTGAACCGGTTTG
42037 AACCGGT
1 -ACCGGT
42044 CTGACCCGAC
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
28 8 0.14
29 41 0.73
30 7 0.12
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.29
Consensus pattern (28 bp):
ACCGGTTTAACCGGTTTGAACCGGTTTG
Found at i:42047 original size:10 final size:10
Alignment explanation
Indices: 41950--42043 Score: 106
Period size: 10 Copynumber: 9.7 Consensus size: 10
41940 GGCTACTGGA
41950 AACCGGTTT-
1 AACCGGTTTG
*
41959 AACCGGTTTTT
1 AACCGG-TTTG
41970 AACCGGTTTG
1 AACCGGTTTG
*
41980 -ACCGGTTTC
1 AACCGGTTTG
*
41989 AACCGGTTCG
1 AACCGGTTTG
41999 AACCGGTTTG
1 AACCGGTTTG
*
42009 -ACCGGTCTG
1 AACCGGTTTG
42018 AACCGGTTTG
1 AACCGGTTTG
*
42028 -ACCGGTCTG
1 AACCGGTTTG
42037 AACCGGT
1 AACCGGT
42044 CTGACCCGAC
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
9 30 0.42
10 36 0.50
11 6 0.08
ACGTcount: A:0.18, C:0.26, G:0.28, T:0.29
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:42067 original size:17 final size:17
Alignment explanation
Indices: 42045--42105 Score: 77
Period size: 17 Copynumber: 3.3 Consensus size: 17
42035 TGAACCGGTC
42045 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
42062 TGACCCGACCTGACCCGACCGT
1 TGA--C--CC-GACCCGACCGT
42084 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
42101 TGACC
1 TGACC
42106 GTTGACCGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 19 0.49
18 2 0.05
19 1 0.03
20 1 0.03
21 2 0.05
22 14 0.36
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:42071 original size:22 final size:22
Alignment explanation
Indices: 42046--42112 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
42036 GAACCGGTCT
42046 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
42068 GACCTGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
42090 GACCCGACCGTTGACCGTTGACC
1 GACCCGACC--CGACCGTTGACC
42113 GTTGACCGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 29 0.73
24 11 0.28
ACGTcount: A:0.18, C:0.45, G:0.24, T:0.13
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:42105 original size:7 final size:7
Alignment explanation
Indices: 42095--42125 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
42085 GACCCGACCC
42095 GACCGTT
1 GACCGTT
42102 GACCGTT
1 GACCGTT
42109 GACCGTT
1 GACCGTT
42116 GACCGTT
1 GACCGTT
42123 GAC
1 GAC
42126 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:42105 original size:12 final size:12
Alignment explanation
Indices: 42051--42093 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
42041 GGTCTGACCC
42051 GACCCGACCGTT
1 GACCCGACCGTT
42063 GACCCGACC--T
1 GACCCGACCGTT
42073 GACCCGACCGTT
1 GACCCGACCGTT
42085 GACCCGACC
1 GACCCGACC
42094 CGACCGTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.34
12 19 0.66
ACGTcount: A:0.19, C:0.47, G:0.23, T:0.12
Consensus pattern (12 bp):
GACCCGACCGTT
Found at i:45557 original size:70 final size:72
Alignment explanation
Indices: 45392--45565 Score: 192
Period size: 70 Copynumber: 2.4 Consensus size: 72
45382 ATCAATAAGA
* * * *
45392 AACAAATGTTGGGGTATGCTGAAAGCCCATTTCAATCATAATCAGGAATATCGACGTGTTTTGAA
1 AACAAATATTGGGGCATGCTGAAAGCCCATTTCAATCAAAATCAGGAATA-C-ACG-ATTTTGAA
*
45457 TGTTCACGTC
63 TGTTCACATC
* * *
45467 AACAAATACTAGGGCATGCTGAAAGCCCATTTCAATCAGAAAT-TGGAATA-AC-ATTTTGAATG
1 AACAAATATTGGGGCATGCTGAAAGCCCATTTCAATCA-AAATCAGGAATACACGATTTTGAATG
*
45529 TTCATATC
65 TTCACATC
* *
45537 AGCAAATATTGGGGCATGCTGAAGGCCCA
1 AACAAATATTGGGGCATGCTGAAAGCCCA
45566 CATCATCATG
Statistics
Matches: 85, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
70 40 0.47
72 2 0.02
75 40 0.47
76 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.28
Consensus pattern (72 bp):
AACAAATATTGGGGCATGCTGAAAGCCCATTTCAATCAAAATCAGGAATACACGATTTTGAATGT
TCACATC
Found at i:46934 original size:22 final size:22
Alignment explanation
Indices: 46906--46984 Score: 131
Period size: 22 Copynumber: 3.6 Consensus size: 22
46896 ACATCTACAT
46906 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
46928 TCTTCAAATATGGTAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
46950 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
46972 TTTTCAAAGATGA
1 TCTTCAAAGATGA
46985 AAGCCTTATT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:47802 original size:48 final size:46
Alignment explanation
Indices: 47654--47966 Score: 425
Period size: 45 Copynumber: 6.8 Consensus size: 46
47644 CTATTTCCCA
* *
47654 CATCTGTAAGCCCTTCAGTGCATGATATTTTC-AAAGCCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
47699 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* * **
47744 CATTTGTAAGCCCTTCAGTGCATGATATTTTCAAAAAAACCTTCAAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC--AAAAACCTTCGGGT
47792 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
47837 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAATAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-A-AAAACCTTCGGGT
** * * * *
47885 CATCCATAAGACCTTTAGTGCAGGATGTTTTCAAAAAGCTTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAA-CCTTCGGGT
* * *
47932 CATCCGTAAGACCTTCAGTGCAGGATGTTTTCAAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
47967 TGAGATTTTA
Statistics
Matches: 243, Mismatches: 18, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
45 116 0.48
46 4 0.02
47 42 0.17
48 81 0.33
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.33
Consensus pattern (46 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
Found at i:47815 original size:93 final size:93
Alignment explanation
Indices: 47654--47966 Score: 443
Period size: 93 Copynumber: 3.4 Consensus size: 93
47644 CTATTTCCCA
*
47654 CATCTGTAAGCCCTTCAGTGCATGATATTTTC---AAAGCCTTCGGGTCATCTGTAAGCCCTTCA
1 CATCTGTAAGCCCTTCAGTGCATGATATTTTCAAAAAAACCTTCGGGTCATCTGTAAGCCCTTCA
47716 GTGCATGATGTTTTCAAAACCTTCGGGT
66 GTGCATGATGTTTTCAAAACCTTCGGGT
* **
47744 CATTTGTAAGCCCTTCAGTGCATGATATTTTCAAAAAAACCTTCAAGTCATCTGTAAGCCCTTCA
1 CATCTGTAAGCCCTTCAGTGCATGATATTTTCAAAAAAACCTTCGGGTCATCTGTAAGCCCTTCA
47809 GTGCATGATGTTTTCAAAACCTTCGGGT
66 GTGCATGATGTTTTCAAAACCTTCGGGT
* * ** * *
47837 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAATAAAACCTTCGGGTCATCCATAAGACCTTTA
1 CATCTGTAAGCCCTTCAGTGCATGATATTTTCAAAAAAACCTTCGGGTCATCTGTAAGCCCTTCA
* *
47902 GTGCAGGATGTTTTCAAAAAGCTTTCGGGT
66 GTGCATGATGTTTTC-AAAA-CCTTCGGGT
* * * *
47932 CATCCGTAAGACCTTCAGTGCAGGATGTTTTCAAA
1 CATCTGTAAGCCCTTCAGTGCATGATATTTTCAAA
47967 TGAGATTTTA
Statistics
Matches: 199, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
90 31 0.16
93 125 0.63
94 4 0.02
95 39 0.20
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.33
Consensus pattern (93 bp):
CATCTGTAAGCCCTTCAGTGCATGATATTTTCAAAAAAACCTTCGGGTCATCTGTAAGCCCTTCA
GTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:48225 original size:3 final size:3
Alignment explanation
Indices: 48217--48303 Score: 102
Period size: 3 Copynumber: 29.0 Consensus size: 3
48207 TTTTTTCATT
* * * *
48217 TTA TTA TTA TAA TTA TTA TTA TAA ATA TTA TTA TTA TTG TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
48265 TTA TTA TTA TTA TTA TTA CTA TAA ATA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
48304 CAGGCCAAAT
Statistics
Matches: 70, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:48366 original size:21 final size:21
Alignment explanation
Indices: 48342--48424 Score: 132
Period size: 21 Copynumber: 4.0 Consensus size: 21
48332 AATTACAAAC
48342 GAGGCCCAGATCTAGAACCCG
1 GAGGCCCAGATCTAGAACCCG
48363 GAGGCCCAGATCTAGAACCCG
1 GAGGCCCAGATCTAGAACCCG
* *
48384 GAGGCCTAGATCCAGAACCCG
1 GAGGCCCAGATCTAGAACCCG
*
48405 GAGGCCCATATCTAG-ACCCG
1 GAGGCCCAGATCTAGAACCCG
48425 ACTCAACACC
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
20 5 0.09
21 52 0.91
ACGTcount: A:0.28, C:0.34, G:0.28, T:0.11
Consensus pattern (21 bp):
GAGGCCCAGATCTAGAACCCG
Found at i:50760 original size:14 final size:14
Alignment explanation
Indices: 50741--50774 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
50731 GCAATCTACA
50741 TGATATTACATATG
1 TGATATTACATATG
*
50755 TGATATTACGTATG
1 TGATATTACATATG
*
50769 TTATAT
1 TGATAT
50775 GATATAACAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.47
Consensus pattern (14 bp):
TGATATTACATATG
Found at i:52657 original size:44 final size:44
Alignment explanation
Indices: 52609--52924 Score: 215
Period size: 44 Copynumber: 7.2 Consensus size: 44
52599 TTTTTTATGA
* *
52609 AAACGCCGCAATAGGTTTGGTATTTAGTGGCGTTTTTAGGGTAC
1 AAACGCCGCAATAGGTTTGGTATTTAGCGGCGTTTTTAGGATAC
* * ** * * * *
52653 AAACGCCGCTACAGGACTAGAATATAGCGGCATTTTTAGGATAC
1 AAACGCCGCAATAGGTTTGGTATTTAGCGGCGTTTTTAGGATAC
* * * * * * *
52697 AAATGCCACGATAGGTATGGTATTTAGCGGCATTTTTAGGGTAA
1 AAACGCCGCAATAGGTTTGGTATTTAGCGGCGTTTTTAGGATAC
* ** * * * *
52741 AAACGCCGCTATAGGACTGGAATATAGTGGTGTTTTTAGGATAC
1 AAACGCCGCAATAGGTTTGGTATTTAGCGGCGTTTTTAGGATAC
* * * * * *
52785 AAACGCCGCGATAAGTATGCTATATAGCGGCATTTTTAGGATAC
1 AAACGCCGCAATAGGTTTGGTATTTAGCGGCGTTTTTAGGATAC
* * * * * **
52829 AAATGCCACTAA-AAG-TTGGTACTTGGCGGCGTTTTT-TTATAC
1 AAACGCCGC-AATAGGTTTGGTATTTAGCGGCGTTTTTAGGATAC
** * **
52871 AAACGCCGCAATAGGTGTTAATATTTCGCGGCGTTTTTCTGATAC
1 AAACGCCGCAATAGGT-TTGGTATTTAGCGGCGTTTTTAGGATAC
52916 AAACGCCGC
1 AAACGCCGC
52925 TAAATATGTG
Statistics
Matches: 206, Mismatches: 61, Indels: 9
0.75 0.22 0.03
Matches are distributed among these distances:
41 2 0.01
42 13 0.06
43 15 0.07
44 161 0.78
45 15 0.07
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (44 bp):
AAACGCCGCAATAGGTTTGGTATTTAGCGGCGTTTTTAGGATAC
Found at i:52685 original size:88 final size:88
Alignment explanation
Indices: 52609--52824 Score: 279
Period size: 88 Copynumber: 2.5 Consensus size: 88
52599 TTTTTTATGA
* * * * *
52609 AAACGCCGCAATAGGTTTGGTATTTAGTGGCGTTTTTAGGGTACAAACGCCGCTACAGGACTAGA
1 AAACGCCACAATAGGTATGGTATTTAGCGGCATTTTTAGGGTAAAAACGCCGCTACAGGACTAGA
52674 ATATAGCGGCATTTTTAGGATAC
66 ATATAGCGGCATTTTTAGGATAC
* * * *
52697 AAATGCCACGATAGGTATGGTATTTAGCGGCATTTTTAGGGTAAAAACGCCGCTATAGGACTGGA
1 AAACGCCACAATAGGTATGGTATTTAGCGGCATTTTTAGGGTAAAAACGCCGCTACAGGACTAGA
* **
52762 ATATAGTGGTGTTTTTAGGATAC
66 ATATAGCGGCATTTTTAGGATAC
* * * * *
52785 AAACGCCGCGATAAGTATGCTATATAGCGGCATTTTTAGG
1 AAACGCCACAATAGGTATGGTATTTAGCGGCATTTTTAGG
52825 ATACAAATGC
Statistics
Matches: 111, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
88 111 1.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (88 bp):
AAACGCCACAATAGGTATGGTATTTAGCGGCATTTTTAGGGTAAAAACGCCGCTACAGGACTAGA
ATATAGCGGCATTTTTAGGATAC
Found at i:52744 original size:132 final size:128
Alignment explanation
Indices: 52608--52927 Score: 336
Period size: 132 Copynumber: 2.4 Consensus size: 128
52598 TTTTTTTATG
*
52608 AAAACGCCGCAATAGGTTTGGTATTTAGTGGCGTTTTTAGGGTACAAACGCCGCTACAGGACTAG
1 AAAACGCCGCAATAGGTTTGGTATTTAGTGGCGTTTTTAGGATACAAACGCCGCTA-AGGA-T-G
* * *
52673 -AATATAGCGGCATTTTTAGGATACAAATGCCACGATAGGTATGGTATTTAGCGGCATTTTTAGG
63 CAATATAGCGGCATTTTTAGGATACAAATGCCACGAAAAGT-TGGTACTTAGCGGCATTTTT-GG
*
52737 GTA
126 ATA
* ** * * * *
52740 AAAACGCCGCTATAGGACTGGAATATAGTGGTGTTTTTAGGATACAAACGCCGCGATAAGTATGC
1 AAAACGCCGCAATAGGTTTGGTATTTAGTGGCGTTTTTAGGATACAAACGCCGC--TAAGGATGC
* * * * **
52805 TATATAGCGGCATTTTTAGGATACAAATGCCACTAAAAGTTGGTACTTGGCGGCGTTTTTTTATA
64 AATATAGCGGCATTTTTAGGATACAAATGCCACGAAAAGTTGGTACTTAGCGGCATTTTTGGATA
* ** * * **
52870 CAAACGCCGCAATAGGTGTTAATATTTCGCGGCGTTTTTCTGATACAAACGCCGCTAA
1 AAAACGCCGCAATAGGT-TTGGTATTTAGTGGCGTTTTTAGGATACAAACGCCGCTAA
52928 ATATGTGACA
Statistics
Matches: 153, Mismatches: 31, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
129 3 0.02
130 16 0.10
131 45 0.29
132 84 0.55
133 3 0.02
134 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (128 bp):
AAAACGCCGCAATAGGTTTGGTATTTAGTGGCGTTTTTAGGATACAAACGCCGCTAAGGATGCAA
TATAGCGGCATTTTTAGGATACAAATGCCACGAAAAGTTGGTACTTAGCGGCATTTTTGGATA
Found at i:59284 original size:230 final size:230
Alignment explanation
Indices: 58881--59341 Score: 859
Period size: 230 Copynumber: 2.0 Consensus size: 230
58871 AAAATATATA
58881 TATATATATTGAATAACTCATCATCATGAATCATGAATTCAGCTTAAAACAATATAATTAATCCC
1 TATATATATTGAATAACTCATCATCATGAATCATGAATTCAGCTTAAAACAATATAATTAATCCC
* *
58946 AAAAGGCTTGAATTCATCTAACTTTTTTTCCGGCAGTAAATCCTAACTCGAACCAAACAATAAAT
66 AAAAGGCTTCAATTCATCTAACTTTTTTTCCGGCAGTAAATCCTAACTCAAACCAAACAATAAAT
59011 TTTCAGGAAAAGAAAATATCTAGTGTCAATATTTAAGTAGAGTATCGATTCCAACTGACAATTTT
131 TTTCAGGAAAAGAAAATATCTAGTGTCAATATTTAAGTAGAGTATCGATTCCAACTGACAATTTT
59076 AAGCTATGGGCCTTGTTGAGTAAGGGTCTTATTAT
196 AAGCTATGGGCCTTGTTGAGTAAGGGTCTTATTAT
*
59111 TATATATATTGAATAACTCATCATCCTGAATCATGAATTCAGCTTAAAACAATATAATTAATCCC
1 TATATATATTGAATAACTCATCATCATGAATCATGAATTCAGCTTAAAACAATATAATTAATCCC
* * *
59176 AAAAGGCTTCAGTTCATTTAACTTTTTTTTCGGCAGTAAATCCTAACTCAAACCAAACAATAAAT
66 AAAAGGCTTCAATTCATCTAACTTTTTTTCCGGCAGTAAATCCTAACTCAAACCAAACAATAAAT
*
59241 TTTCAGGAAAAGAAAATATCTAGTGTCAATATTTAAGTAGAGTATCGATTCCAATTGACAATTTT
131 TTTCAGGAAAAGAAAATATCTAGTGTCAATATTTAAGTAGAGTATCGATTCCAACTGACAATTTT
59306 AAGCTATGGGCCTTGTTGAGTAAGGGTCTTATTAT
196 AAGCTATGGGCCTTGTTGAGTAAGGGTCTTATTAT
59341 T
1 T
59342 GATCATGGTG
Statistics
Matches: 224, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
230 224 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (230 bp):
TATATATATTGAATAACTCATCATCATGAATCATGAATTCAGCTTAAAACAATATAATTAATCCC
AAAAGGCTTCAATTCATCTAACTTTTTTTCCGGCAGTAAATCCTAACTCAAACCAAACAATAAAT
TTTCAGGAAAAGAAAATATCTAGTGTCAATATTTAAGTAGAGTATCGATTCCAACTGACAATTTT
AAGCTATGGGCCTTGTTGAGTAAGGGTCTTATTAT
Found at i:60463 original size:32 final size:32
Alignment explanation
Indices: 60382--60463 Score: 112
Period size: 32 Copynumber: 2.6 Consensus size: 32
60372 GAATATTCGA
**
60382 ATAGATAAATATTTATTTGTCACTAAAGACAC
1 ATAGATAAATACATATTTGTCACTAAAGACAC
**
60414 ATAGATAAATATTTATTTGTCACTAAAGACAC
1 ATAGATAAATACATATTTGTCACTAAAGACAC
60446 ATAGAT-AATCACATATTT
1 ATAGATAAAT-ACATATTT
60464 CAATCACCAC
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
31 3 0.06
32 44 0.94
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (32 bp):
ATAGATAAATACATATTTGTCACTAAAGACAC
Found at i:60463 original size:36 final size:32
Alignment explanation
Indices: 60382--60453 Score: 144
Period size: 32 Copynumber: 2.2 Consensus size: 32
60372 GAATATTCGA
60382 ATAGATAAATATTTATTTGTCACTAAAGACAC
1 ATAGATAAATATTTATTTGTCACTAAAGACAC
60414 ATAGATAAATATTTATTTGTCACTAAAGACAC
1 ATAGATAAATATTTATTTGTCACTAAAGACAC
60446 ATAGATAA
1 ATAGATAA
60454 TCACATATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.33
Consensus pattern (32 bp):
ATAGATAAATATTTATTTGTCACTAAAGACAC
Found at i:63497 original size:18 final size:18
Alignment explanation
Indices: 63476--63516 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
63466 CGACCCATTT
*
63476 ACCCGACCTGCTGACCCG
1 ACCCGACCCGCTGACCCG
*
63494 ACCCGACCCGTTGACCCG
1 ACCCGACCCGCTGACCCG
63512 ACCCG
1 ACCCG
63517 TTGACCGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.51, G:0.22, T:0.10
Consensus pattern (18 bp):
ACCCGACCCGCTGACCCG
Found at i:63509 original size:13 final size:13
Alignment explanation
Indices: 63493--63522 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
63483 CTGCTGACCC
63493 GACCCGACCCGTT
1 GACCCGACCCGTT
63506 GACCCGACCCGTT
1 GACCCGACCCGTT
63519 GACC
1 GACC
63523 GTTGACCTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:63522 original size:31 final size:31
Alignment explanation
Indices: 63458--63522 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
63448 ACCGGTCATA
* *
63458 ACCCGACCCGACCCATTTACCCGACCTGCTG
1 ACCCGACCCGACCCATTGACCCGACCCGCTG
* *
63489 ACCCGACCCGACCCGTTGACCCGACCCGTTG
1 ACCCGACCCGACCCATTGACCCGACCCGCTG
63520 ACC
1 ACC
63523 GTTGACCTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.18, C:0.49, G:0.18, T:0.14
Consensus pattern (31 bp):
ACCCGACCCGACCCATTGACCCGACCCGCTG
Found at i:63526 original size:20 final size:20
Alignment explanation
Indices: 63501--63542 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
63491 CCGACCCGAC
63501 CCGTTGACCCGACCCGTTGA
1 CCGTTGACCCGACCCGTTGA
* *
63521 CCGTTGACCTGACCTGTTGA
1 CCGTTGACCCGACCCGTTGA
63541 CC
1 CC
63543 ACTGTTGACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.38, G:0.24, T:0.24
Consensus pattern (20 bp):
CCGTTGACCCGACCCGTTGA
Found at i:66047 original size:24 final size:24
Alignment explanation
Indices: 65924--66035 Score: 145
Period size: 24 Copynumber: 4.7 Consensus size: 24
65914 ATTTGAATTA
65924 TGATCTGATACTTGACATGGATTC
1 TGATCTGATACTTGACATGGATTC
*
65948 TTATCTGATA-TCTGACATGGATTC
1 TGATCTGATACT-TGACATGGATTC
* *
65972 TGATTTGATACTTGACTTGGATTC
1 TGATCTGATACTTGACATGGATTC
* * *
65996 TGATCTGTTACTTGACCTGGATTT
1 TGATCTGATACTTGACATGGATTC
*
66020 TGATATGATACTTGAC
1 TGATCTGATACTTGAC
66036 GTGAATTATG
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
23 1 0.01
24 74 0.97
25 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.42
Consensus pattern (24 bp):
TGATCTGATACTTGACATGGATTC
Found at i:70631 original size:24 final size:24
Alignment explanation
Indices: 70503--70614 Score: 145
Period size: 24 Copynumber: 4.7 Consensus size: 24
70493 ATTTGAATTA
*
70503 TGATCTGATACTTGACATGGATTC
1 TGATCTGATACTTGACTTGGATTC
70527 TGATCTGATA-TCTGACTTGGATTC
1 TGATCTGATACT-TGACTTGGATTC
70551 TGATCTGATACTTGACTTGGATTC
1 TGATCTGATACTTGACTTGGATTC
* * * *
70575 TGATATGTTACTTGACCTGGATTT
1 TGATCTGATACTTGACTTGGATTC
* *
70599 TTATATGATACTTGAC
1 TGATCTGATACTTGAC
70615 GTGAATTATG
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
23 1 0.01
24 77 0.97
25 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.42
Consensus pattern (24 bp):
TGATCTGATACTTGACTTGGATTC
Found at i:72449 original size:83 final size:83
Alignment explanation
Indices: 72344--72535 Score: 269
Period size: 83 Copynumber: 2.3 Consensus size: 83
72334 TTTTTTTTGC
* * * * * * *
72344 ACAAACTCCACAATAAATAATACTATTGTGGCGTTTGTTTGACAATCGCCGCGAAAGT-ACTTCT
1 ACAAACGCCACTATAAACAATACTATTGCGGCGTTTGTCTGACAAACACCGCGAAA-TAACTTCT
*
72408 CTATAGCGTCGTTTGTTGA
65 CTATAGCGTCGCTTGTTGA
*
72427 ACAAACGCCACTATAAACAATACTATTGCGGCGTTTGTCTGATAAACACCGCGAAATAACTTCTC
1 ACAAACGCCACTATAAACAATACTATTGCGGCGTTTGTCTGACAAACACCGCGAAATAACTTCTC
72492 TATAGCGTCGCTTGTTGA
66 TATAGCGTCGCTTGTTGA
* *
72510 ACAAATGCCACTATAAACAACACTAT
1 ACAAACGCCACTATAAACAATACTAT
72536 CACGGCATTT
Statistics
Matches: 97, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
82 1 0.01
83 96 0.99
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.29
Consensus pattern (83 bp):
ACAAACGCCACTATAAACAATACTATTGCGGCGTTTGTCTGACAAACACCGCGAAATAACTTCTC
TATAGCGTCGCTTGTTGA
Found at i:72669 original size:83 final size:82
Alignment explanation
Indices: 72406--72669 Score: 266
Period size: 83 Copynumber: 3.2 Consensus size: 82
72396 GAAAGTACTT
72406 CTCTATAGCGTCGTTTGTTGAACAAACGCCACTATAAACAAT-ACTATTGCGGCG-TTTGTCTGA
1 CTCTATAGCGTCGTTTGTTGAACAAACGCCACTATAAAC-ATCACTATTGCGGCGTTTTG-CT-A
* * * **
72469 TAAACACCGCGAAATAACTT
63 TAAACGCCGCTAAATTACCA
* * * ** * *
72489 CTCTATAGCGTCGCTTGTTGAACAAATGCCACTATAAACAACACTATCACGGCATTTGTG-TAAA
1 CTCTATAGCGTCGTTTGTTGAACAAACGCCACTATAAACATCACTATTGCGGCGTTT-TGCTATA
*
72553 AACGCCGTTAAATTACCA
65 AACGCCGCTAAATTACCA
* * * * *
72571 CTCTATTGAGACGTTTGTTGAGA-AAACGCCACTTTAAACATCTCTATTGCGGCGTTTTAGCTAT
1 CTCTATAGCGTCGTTTGTTGA-ACAAACGCCACTATAAACATCACTATTGCGGCGTTTT-GCTAT
72635 AAACGCCGCTAAATTACCA
64 AAACGCCGCTAAATTACCA
* *
72654 CTCTATTGCGGCGTTT
1 CTCTATAGCGTCGTTT
72670 TTTTAAAAAA
Statistics
Matches: 147, Mismatches: 28, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
81 1 0.01
82 60 0.41
83 82 0.56
84 2 0.01
85 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (82 bp):
CTCTATAGCGTCGTTTGTTGAACAAACGCCACTATAAACATCACTATTGCGGCGTTTTGCTATAA
ACGCCGCTAAATTACCA
Found at i:74235 original size:21 final size:20
Alignment explanation
Indices: 74192--74233 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
74182 AGAAAATACA
*
74192 TATTATATACTTTGTATTTT
1 TATTATATACTTTATATTTT
74212 TATTAATATTACTTTATATTTT
1 TATT-ATA-TACTTTATATTTT
74234 ATATATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 3 0.16
22 12 0.63
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (20 bp):
TATTATATACTTTATATTTT
Found at i:74328 original size:15 final size:16
Alignment explanation
Indices: 74310--74343 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
74300 TTAAACTTTT
74310 TTAAAATTTT-AATAA
1 TTAAAATTTTAAATAA
*
74325 TTAATATTTTAAATAA
1 TTAAAATTTTAAATAA
74341 TTA
1 TTA
74344 TAGCAAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAAATTTTAAATAA
Done.