Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013168.1 Corchorus capsularis cultivar CVL-1 contig13189, 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: 86582
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:2154 original size:76 final size:84
Alignment explanation
Indices: 1910--2281 Score: 382
Period size: 86 Copynumber: 4.5 Consensus size: 84
1900 TAATAATGGA
* * * * *
1910 AATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGACATATTTTAAGGAATAAA-ATA-AT
1 AATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAAGAGATATTTTAAGAAACAAATAAATAT
* *
1973 -AA-ATTTATAA-A-AAGAG
66 AAAGATTGA-AAGATATGAG
* *
1989 AATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAAATAAATAAAT-
1 AATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAAGAGATATTTTAAG-AAACAAATAAATA
* * *
2053 TAAAAATAGAATTA-ATAATGTG
65 TAAAGATTGAA--AGAT-ATGAG
* *
2075 AATATTTCCTAAATCTTGCCAAATTGTGGGAGATTTAAGAGATATTTTAAGAAA-TAA-AAATA-
1 AATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAAGAGATATTTTAAGAAACAAATAAATAT
*
2137 ATA-A-T-AAAG-T-TGAG
66 AAAGATTGAAAGATATGAG
* *
2151 AATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGAAACAAATAAATAT
1 AATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAAGAGATATTTTAAGAAACAAATAAATA-
*
2216 TAAAGATTGAATGATAATGAG
65 TAAAGATTGAAAGAT-ATGAG
*
2237 AATATTTTCTAAATCTTGTCAAATTGTGGGAGATTT-AGAAGATAT
1 AATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAAG-AGATAT
2282 AAAAGGAAAT
Statistics
Matches: 249, Mismatches: 22, Indels: 37
0.81 0.07 0.12
Matches are distributed among these distances:
76 54 0.22
77 2 0.01
78 7 0.03
79 50 0.20
80 10 0.04
81 4 0.02
82 5 0.02
83 12 0.05
84 5 0.02
85 4 0.02
86 96 0.39
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.35
Consensus pattern (84 bp):
AATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAAGAGATATTTTAAGAAACAAATAAATAT
AAAGATTGAAAGATATGAG
Found at i:2242 original size:162 final size:163
Alignment explanation
Indices: 1900--2281 Score: 533
Period size: 162 Copynumber: 2.3 Consensus size: 163
1890 ATTGTTAAAA
* * *
1900 TAATAATGGAAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGACATATTTTAAGGAAT
1 TAATAATGG-AATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAAGAGATATTTTAAGAAAT
*
1965 AAAATAATAAATTTATAAAAAGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAG
65 AAAATAATAAA-TTATAAAAAGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAG
*
2030 ATATTTTAAGAAAATAAATAAATTAAAAATAGAAT
129 ATATTTTAAGAAAACAAATAAATTAAAAATAGAAT
*
2065 TAATAATGTGAATATTTCCTAAATCTTGCCAAATTGTGGGAGATTTAAGAGATATTTTAAGAAAT
1 TAATAATG-GAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAAGAGATATTTTAAGAAAT
***
2130 AAAAATAAT-AA-TA-AAGTTGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAG
65 -AAAATAATAAATTATAAAAAGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAG
* *
2192 ATATTTTAAG-AAACAAATAAATATTAAAGATTGAA-
129 ATATTTTAAGAAAACAAAT-AA-ATTAAAAATAGAAT
* *
2227 TGATAATGAGAATATTTTCTAAATCTTGTCAAATTGTGGGAGATTT-AGAAGATAT
1 TAATAATG-GAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAAG-AGATAT
2282 AAAAGGAAAT
Statistics
Matches: 197, Mismatches: 15, Indels: 13
0.88 0.07 0.06
Matches are distributed among these distances:
161 9 0.05
162 105 0.53
163 13 0.07
165 61 0.31
166 9 0.05
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.35
Consensus pattern (163 bp):
TAATAATGGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAAGAGATATTTTAAGAAATA
AAATAATAAATTATAAAAAGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGAT
ATTTTAAGAAAACAAATAAATTAAAAATAGAAT
Found at i:10484 original size:33 final size:33
Alignment explanation
Indices: 10437--10510 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
10427 CTAATTGTGA
* *
10437 TGAAAACAAATCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
*
10470 TGCAAATAATTCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
10503 TGAAAATA
1 TGAAAATA
10511 GGACTGTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.38
Consensus pattern (33 bp):
TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
Found at i:10518 original size:33 final size:33
Alignment explanation
Indices: 10448--10522 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 33
10438 GAAAACAAAT
* **
10448 CTGTTTTGGTTGATCATAGCATTGCAAATAATT
1 CTGTTTTGGTTGATCATAGCATTGAAAATAAGA
*
10481 CTGTTTTGGTTGATCATAGCATTGAAAATAGGA
1 CTGTTTTGGTTGATCATAGCATTGAAAATAAGA
10514 CTGTTTTGG
1 CTGTTTTGG
10523 GTAAAAAGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.25, C:0.11, G:0.23, T:0.41
Consensus pattern (33 bp):
CTGTTTTGGTTGATCATAGCATTGAAAATAAGA
Found at i:22099 original size:7 final size:7
Alignment explanation
Indices: 22082--22111 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
22072 TGTAAATGCA
22082 AAATAAT
1 AAATAAT
22089 -AATAAT
1 AAATAAT
22095 AAATAAT
1 AAATAAT
22102 AAATAAT
1 AAATAAT
22109 AAA
1 AAA
22112 AAAGAAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAATAAT
Found at i:23047 original size:22 final size:22
Alignment explanation
Indices: 23006--23084 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
22996 GCCCAACATG
*
23006 TTTTGATAGAATATTTTTATGAAA
1 TTTTGATA-ATTA-TTTTATGAAA
* *
23030 TTTTAATAATTATTTTATTAAA
1 TTTTGATAATTATTTTATGAAA
* ***
23052 TTTTGATAACTACACTATGAAA
1 TTTTGATAATTATTTTATGAAA
23074 TTTTGATAATT
1 TTTTGATAATT
23085 TACCTATAAA
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
22 35 0.78
23 3 0.07
24 7 0.16
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.51
Consensus pattern (22 bp):
TTTTGATAATTATTTTATGAAA
Found at i:23091 original size:22 final size:21
Alignment explanation
Indices: 23023--23097 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 21
23013 AGAATATTTT
* **
23023 TATGAAATTTTAATAATTATTT
1 TATGAAATTTTGATAATTA-CC
* *
23045 TATTAAATTTTGATAACTACAC
1 TATGAAATTTTGATAATTAC-C
23067 TATGAAATTTTGATAATTTACC
1 TATGAAATTTTGATAA-TTACC
*
23089 TATAAAATT
1 TATGAAATT
23098 GTTATAAACT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
22 40 0.93
23 3 0.07
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (21 bp):
TATGAAATTTTGATAATTACC
Found at i:23200 original size:20 final size:22
Alignment explanation
Indices: 23180--23237 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 22
23170 GTAACCTTCC
*
23180 TATGA-TTTTTGATAATCTCCT
1 TATGAGTTTTTGATAATCTCCG
* * *
23201 TGTGAGATTTTGTTAATCTCCG
1 TATGAGTTTTTGATAATCTCCG
* *
23223 TATAATTTTTTGATA
1 TATGAGTTTTTGATA
23238 CTATAGTAAG
Statistics
Matches: 27, Mismatches: 9, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.52
Consensus pattern (22 bp):
TATGAGTTTTTGATAATCTCCG
Found at i:26357 original size:7 final size:7
Alignment explanation
Indices: 26345--26385 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
26335 CTCGGAGGTC
26345 AAAGTCA
1 AAAGTCA
26352 AAAGTCA
1 AAAGTCA
*
26359 ACAGTC-
1 AAAGTCA
26365 AAAGTCA
1 AAAGTCA
*
26372 ACAG-CA
1 AAAGTCA
26378 AAAGTCA
1 AAAGTCA
26385 A
1 A
26386 TGCTGACGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 10 0.36
7 18 0.64
ACGTcount: A:0.54, C:0.20, G:0.15, T:0.12
Consensus pattern (7 bp):
AAAGTCA
Found at i:26368 original size:13 final size:14
Alignment explanation
Indices: 26342--26385 Score: 67
Period size: 13 Copynumber: 3.4 Consensus size: 14
26332 AGTCTCGGAG
26342 GTCAA-AGTCAAAA
1 GTCAACAGTCAAAA
26355 GTCAACAGTC-AAA
1 GTCAACAGTCAAAA
26368 GTCAACAG-CAAAA
1 GTCAACAGTCAAAA
26381 GTCAA
1 GTCAA
26386 TGCTGACGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 1 0.03
13 24 0.83
14 4 0.14
ACGTcount: A:0.50, C:0.20, G:0.16, T:0.14
Consensus pattern (14 bp):
GTCAACAGTCAAAA
Found at i:27239 original size:2 final size:2
Alignment explanation
Indices: 27232--27261 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
27222 TATACATAGA
27232 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
27262 TAACAAGTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27461 original size:16 final size:16
Alignment explanation
Indices: 27438--27472 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
27428 AAAAATTAAG
*
27438 AGAAAAAGGAAA-AAA
1 AGAAAAAAGAAAGAAA
27453 AGAAAAAAGAAAGAAA
1 AGAAAAAAGAAAGAAA
27469 AGAA
1 AGAA
27473 TTTGCCTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (16 bp):
AGAAAAAAGAAAGAAA
Found at i:30568 original size:2 final size:2
Alignment explanation
Indices: 30561--30593 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
30551 GGAAGCATTA
*
30561 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30594 ATAATAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30599 original size:3 final size:3
Alignment explanation
Indices: 30591--30620 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
30581 ATATATATAT
30591 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
30621 TACTTACTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:33410 original size:12 final size:12
Alignment explanation
Indices: 33395--33420 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
33385 AATATCAAGA
33395 TAAATTTGATAG
1 TAAATTTGATAG
33407 TAAATTTGATAG
1 TAAATTTGATAG
33419 TA
1 TA
33421 TGGGTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (12 bp):
TAAATTTGATAG
Found at i:33476 original size:21 final size:21
Alignment explanation
Indices: 33432--33489 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
33422 GGGTTAAAAG
33432 TGAAAATATAGATATA-TGGA
1 TGAAAATATAGATATATTGGA
*
33452 TGAAAATATAGATATATTTGA
1 TGAAAATATAGATATATTGGA
*
33473 TGAAAATATAAATATAT
1 TGAAAATATAGATATAT
33490 GATGGGGTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 16 0.46
21 19 0.54
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (21 bp):
TGAAAATATAGATATATTGGA
Found at i:34035 original size:2 final size:2
Alignment explanation
Indices: 34015--34105 Score: 57
Period size: 2 Copynumber: 46.0 Consensus size: 2
34005 TATTCAAATA
* *
34015 AT AT AT GT AGT AT AGT AT AT AT AT AT AT A- AT GT AT AT AT AT AT
1 AT AT AT AT A-T AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
34058 AT AT AA ACT A- AT -T CT -T CAT TT AT AT -T AT AT AT AT AT AT TT
1 AT AT AT A-T AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT
34098 AT AT AT AT
1 AT AT AT AT
34106 TCAATTAAAC
Statistics
Matches: 70, Mismatches: 10, Indels: 18
0.71 0.10 0.18
Matches are distributed among these distances:
1 5 0.07
2 59 0.84
3 6 0.09
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34561 original size:45 final size:45
Alignment explanation
Indices: 34497--34582 Score: 172
Period size: 45 Copynumber: 1.9 Consensus size: 45
34487 ACTTCTCCAA
34497 CTCATCATTAATCCAGGGTAGGGATCTTTTAGTAATTCCACCCAG
1 CTCATCATTAATCCAGGGTAGGGATCTTTTAGTAATTCCACCCAG
34542 CTCATCATTAATCCAGGGTAGGGATCTTTTAGTAATTCCAC
1 CTCATCATTAATCCAGGGTAGGGATCTTTTAGTAATTCCAC
34583 TACTATATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (45 bp):
CTCATCATTAATCCAGGGTAGGGATCTTTTAGTAATTCCACCCAG
Found at i:43097 original size:3 final size:3
Alignment explanation
Indices: 43089--43123 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
43079 GATTATCAAG
*
43089 TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
43124 GACTTTGGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:43162 original size:108 final size:108
Alignment explanation
Indices: 43012--43231 Score: 431
Period size: 108 Copynumber: 2.0 Consensus size: 108
43002 ATATAGCACA
43012 ATTAGACTTTGGCAATGGTGCTAACTATGCTTGATATGGATTTCTTCTACCATGCGTTTGTAATT
1 ATTAGACTTTGGCAATGGTGCTAACTATGCTTGATATGGATTTCTTCTACCATGCGTTTGTAATT
43077 CAGATTATCAAGTATTATTATTATTATTATCATTATTATTATT
66 CAGATTATCAAGTATTATTATTATTATTATCATTATTATTATT
43120 ATTAGACTTTGGCAATGGTGCTAACTATGCTTGATATGGATTTCTTCTACCATGCGTTTGTAATT
1 ATTAGACTTTGGCAATGGTGCTAACTATGCTTGATATGGATTTCTTCTACCATGCGTTTGTAATT
*
43185 CAGATTATCAAGTATTATTATTATTATTATTATTATTATTATT
66 CAGATTATCAAGTATTATTATTATTATTATCATTATTATTATT
43228 ATTA
1 ATTA
43232 TTATTATTAT
Statistics
Matches: 111, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 111 1.00
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (108 bp):
ATTAGACTTTGGCAATGGTGCTAACTATGCTTGATATGGATTTCTTCTACCATGCGTTTGTAATT
CAGATTATCAAGTATTATTATTATTATTATCATTATTATTATT
Found at i:43205 original size:3 final size:3
Alignment explanation
Indices: 43197--43241 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
43187 GATTATCAAG
43197 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
43242 ATATACATCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:43517 original size:18 final size:18
Alignment explanation
Indices: 43494--43551 Score: 66
Period size: 17 Copynumber: 3.3 Consensus size: 18
43484 CATAGTAAAG
43494 CTGCCCTAGTGGGGCGGC
1 CTGCCCTAGTGGGGCGGC
* * **
43512 CTGCCC-AATGGTGAAGC
1 CTGCCCTAGTGGGGCGGC
43529 C-GCCCTAGTGGGGCGGC
1 CTGCCCTAGTGGGGCGGC
43546 CTGCCC
1 CTGCCC
43552 ATGGTAAGCC
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
16 4 0.13
17 16 0.53
18 10 0.33
ACGTcount: A:0.10, C:0.36, G:0.38, T:0.16
Consensus pattern (18 bp):
CTGCCCTAGTGGGGCGGC
Found at i:43539 original size:34 final size:33
Alignment explanation
Indices: 43448--43577 Score: 147
Period size: 34 Copynumber: 4.0 Consensus size: 33
43438 ACGTAGTGAG
* *
43448 TGCCC-TGGCGAAGCCGCCCCAGTGGGGCGGCC
1 TGCCCATGGTGAAGCCGCCCTAGTGGGGCGGCC
*** * * *
43480 TATTCATAGTAAAGCTGCCCTAGTGGGGCGGCC
1 TGCCCATGGTGAAGCCGCCCTAGTGGGGCGGCC
43513 TGCCCAATGGTGAAGCCGCCCTAGTGGGGCGGCC
1 TGCCC-ATGGTGAAGCCGCCCTAGTGGGGCGGCC
**
43547 TGCCCATGGT-AAGCCGCCCTCTTGGGGCGGC
1 TGCCCATGGTGAAGCCGCCCTAGTGGGGCGGC
43578 ACGGGTCATC
Statistics
Matches: 80, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
32 21 0.26
33 29 0.36
34 30 0.38
ACGTcount: A:0.14, C:0.33, G:0.36, T:0.17
Consensus pattern (33 bp):
TGCCCATGGTGAAGCCGCCCTAGTGGGGCGGCC
Found at i:44202 original size:37 final size:37
Alignment explanation
Indices: 44161--44240 Score: 106
Period size: 37 Copynumber: 2.2 Consensus size: 37
44151 AATTCCCTTT
* * * *
44161 TTAAAGTGAAAGTAAAACTAATGAGATCTTTCCCAAC
1 TTAAAATGAAACTAAAACTAACGAGATCTTCCCCAAC
* *
44198 TTAAAATGAAACTAAAACTAACGGGATCTTCCCCTAC
1 TTAAAATGAAACTAAAACTAACGAGATCTTCCCCAAC
44235 TTAAAA
1 TTAAAA
44241 CCGAAATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.26
Consensus pattern (37 bp):
TTAAAATGAAACTAAAACTAACGAGATCTTCCCCAAC
Found at i:44251 original size:37 final size:37
Alignment explanation
Indices: 44168--44308 Score: 133
Period size: 38 Copynumber: 3.8 Consensus size: 37
44158 TTTTTAAAGT
* * * * *
44168 GAAAGTAAAACTAATGAGATCTTTCCCAACTTAAAAT
1 GAAACTAAAACTAACGGGATCTTTCCCTACTTAAAAC
*
44205 GAAACTAAAACTAACGGGATCTTCCCCTACTTAAAACC
1 GAAACTAAAACTAACGGGATCTTTCCCTACTTAAAA-C
* * * *
44243 GAAA-TAAAA-AAAGGTGGGATCTTTCCCTCCTTAATGAC
1 GAAACTAAAACTAA--CGGGATCTTTCCCTACTTAA-AAC
*
44281 GAAACTAAAACTAACAGGATCTTTCCCT
1 GAAACTAAAACTAACGGGATCTTTCCCT
44309 TCTTTTGAAA
Statistics
Matches: 84, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
36 2 0.02
37 36 0.43
38 38 0.45
39 6 0.07
40 2 0.02
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.25
Consensus pattern (37 bp):
GAAACTAAAACTAACGGGATCTTTCCCTACTTAAAAC
Found at i:44454 original size:12 final size:11
Alignment explanation
Indices: 44439--44473 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
44429 TCATTTCCAA
44439 TTTTTCTTCTTC
1 TTTTTCTT-TTC
44451 TTTTTCTTTTC
1 TTTTTCTTTTC
44462 TTTTT-TTTTC
1 TTTTTCTTTTC
44472 TT
1 TT
44474 AACCATTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 7 0.30
11 8 0.35
12 8 0.35
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:44984 original size:26 final size:25
Alignment explanation
Indices: 44951--45000 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
44941 CCAAATTTTA
*
44951 TAACTAAAGA-TAAAGCCCCAACCCT
1 TAACTAAA-ACTAAAGCCCAAACCCT
44976 TAACATAAAACTAAAGCCCAAACCC
1 TAAC-TAAAACTAAAGCCCAAACCC
45001 AAAATGTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.48, C:0.32, G:0.06, T:0.14
Consensus pattern (25 bp):
TAACTAAAACTAAAGCCCAAACCCT
Found at i:45105 original size:15 final size:14
Alignment explanation
Indices: 45081--45111 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
45071 CCAAATATTC
45081 TTTTAATTTCTAAA
1 TTTTAATTTCTAAA
45095 TTTTAAATTTCTAAA
1 TTTT-AATTTCTAAA
45110 TT
1 TT
45112 ACTTAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTTAATTTCTAAA
Found at i:48270 original size:19 final size:18
Alignment explanation
Indices: 48237--48272 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
48227 TTGAAATAAT
48237 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
48255 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
48273 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:49846 original size:25 final size:25
Alignment explanation
Indices: 49795--49846 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
49785 TTATTAATGA
* * *
49795 AACTTGAAAAATAAAGACATAAGAT
1 AACTAGAAAAATAAAGACAAAACAT
* *
49820 AACTAGAAAATTAAAGATAAAACAT
1 AACTAGAAAAATAAAGACAAAACAT
49845 AA
1 AA
49847 ACTAAATAAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.63, C:0.08, G:0.10, T:0.19
Consensus pattern (25 bp):
AACTAGAAAAATAAAGACAAAACAT
Found at i:52776 original size:63 final size:61
Alignment explanation
Indices: 52581--52986 Score: 282
Period size: 63 Copynumber: 6.4 Consensus size: 61
52571 GAAAAAATTG
* * *
52581 ACCCTTTGTCCGAAAGGGTATTTTGGGAATAG--AAACTATAT-AAGAGAATGTGACGAAACTG
1 ACCCTTTGTCCGAAAGGGTATTTTGGGAAT-GCTAAACTAAATGCA-AGAATGTGA-GAAACTA
** * * *
52642 ACCCTTTGTTTGAAAGGGTATTTTGGGAA--CTATAATCTAAGTGCAAAAATGTGGAGAAACTG
1 ACCCTTTGTCCGAAAGGGTATTTTGGGAATGCTA-AA-CTAAATGCAAGAATGT-GAGAAACTA
* * * *
52704 ACCATTTGTCTGAAAGAGTATTTTGGGAATGCTAAACTCAAATGCAGGAATGTGATGAAACTA
1 ACCCTTTGTCCGAAAGGGTATTTTGGGAATGCTAAACT-AAATGCAAGAATGTGA-GAAACTA
* * ** *
52767 ACTCTTTGTCCGAAAGGGCATTTTGGGAAACCTTGAAACTAAATGCAAGAATGTGAGAAAACCA
1 ACCCTTTGTCCGAAAGGGTATTTTGGGAATGC-T-AAACTAAATGCAAGAATGTGAG-AAACTA
* ** *
52831 ACCCTTTGTCCGAAAGGGTATTTTTGGGAATCGAAAATACTTAACTTAAATGCGGGAATGTGACA
1 ACCCTTTGTCCGAAAGGGTA-TTTTGGGAAT-G------CTAAAC-TAAATGCAAGAATGTGA-G
*
52896 AAATTA
56 AAACTA
* * * * ** * * * *
52902 GCACTTTGTCTGAAAGGGCATTTTGGGAAAACTAGAACCTAAATGCAAGAAAGTGACAAATTG
1 ACCCTTTGTCCGAAAGGGTATTTTGGGAATGCTA-AA-CTAAATGCAAGAATGTGAGAAACTA
52965 ACCCTTTGTCCGAAAGGGTATT
1 ACCCTTTGTCCGAAAGGGTATT
52987 CAGGAAAAAA
Statistics
Matches: 272, Mismatches: 48, Indels: 48
0.74 0.13 0.13
Matches are distributed among these distances:
60 1 0.00
61 29 0.11
62 47 0.17
63 73 0.27
64 58 0.21
65 15 0.06
70 12 0.04
71 36 0.13
72 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.27
Consensus pattern (61 bp):
ACCCTTTGTCCGAAAGGGTATTTTGGGAATGCTAAACTAAATGCAAGAATGTGAGAAACTA
Found at i:52919 original size:135 final size:134
Alignment explanation
Indices: 52738--52986 Score: 345
Period size: 135 Copynumber: 1.9 Consensus size: 134
52728 GGGAATGCTA
** * * *
52738 AACTCAAATGCAGGAATGTGATGAAACTAACTCTTTGTCCGAAAGGGCATTTTGGGAAACCTTGA
1 AACTCAAATGCAGGAATGTGACAAAACTAACACTTTGTCCGAAAGGGCATTTTGGGAAAACTAGA
*
52803 AACTAAATGCAAGAATGTGAGAAAACCAACCCTTTGTCCGAAAGGGTATTTTTGGGAATCGAAAA
66 AACTAAATGCAAGAAAGTGA-AAAACCAACCCTTTGTCCGAAAGGGTATTTTTGGGAATCGAAAA
52868 TACTT
130 TACTT
* * * * *
52873 AACTTAAATGCGGGAATGTGACAAAATTAGCACTTTGTCTGAAAGGGCATTTTGGGAAAACTAGA
1 AACTCAAATGCAGGAATGTGACAAAACTAACACTTTGTCCGAAAGGGCATTTTGGGAAAACTAGA
* * ***
52938 ACCTAAATGCAAGAAAGTGACAAATTGACCCTTTGTCCGAAAGGGTATT
66 AACTAAATGCAAGAAAGTGAAAAACCAACCCTTTGTCCGAAAGGGTATT
52987 CAGGAAAAAA
Statistics
Matches: 98, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
134 25 0.26
135 73 0.74
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.26
Consensus pattern (134 bp):
AACTCAAATGCAGGAATGTGACAAAACTAACACTTTGTCCGAAAGGGCATTTTGGGAAAACTAGA
AACTAAATGCAAGAAAGTGAAAAACCAACCCTTTGTCCGAAAGGGTATTTTTGGGAATCGAAAAT
ACTT
Found at i:53045 original size:49 final size:48
Alignment explanation
Indices: 52992--53141 Score: 113
Period size: 49 Copynumber: 3.3 Consensus size: 48
52982 GTATTCAGGA
*
52992 AAAAAGCAAGTAAAAATAGGCGCCTTTCGACCGGGAAGGGCGTTTTGGG
1 AAAAAGCAAGTAAAAATA-GCGCCTTTCAACCGGGAAGGGCGTTTTGGG
* * * *
53041 --AAA--AA-T----A-AGTGCCTTCCATCTGGGAAGGGCGTTTTGGG
1 AAAAAGCAAGTAAAAATAGCGCCTTTCAACCGGGAAGGGCGTTTTGGG
** * * *
53079 AAAAAGTTAGTAAAAATAAACACCTTCCAACCGGGAAGGGCGTTTTGGG
1 AAAAAGCAAGTAAAAAT-AGCGCCTTTCAACCGGGAAGGGCGTTTTGGG
*
53128 AAAAAGCAGGTAAA
1 AAAAAGCAAGTAAA
53142 GACTGAAAAT
Statistics
Matches: 76, Mismatches: 14, Indels: 22
0.68 0.12 0.20
Matches are distributed among these distances:
38 25 0.33
39 1 0.01
40 4 0.05
42 1 0.01
43 1 0.01
44 1 0.01
45 2 0.03
47 4 0.05
49 37 0.49
ACGTcount: A:0.36, C:0.15, G:0.29, T:0.20
Consensus pattern (48 bp):
AAAAAGCAAGTAAAAATAGCGCCTTTCAACCGGGAAGGGCGTTTTGGG
Found at i:53055 original size:38 final size:38
Alignment explanation
Indices: 53003--53083 Score: 110
Period size: 38 Copynumber: 2.1 Consensus size: 38
52993 AAAAGCAAGT
* *
53003 AAAAATAGGCGCCTTTCGA-CCGGGAAGGGCGTTTTGGG
1 AAAAATAAGCGCC-TTCCATCCGGGAAGGGCGTTTTGGG
* *
53041 AAAAATAAGTGCCTTCCATCTGGGAAGGGCGTTTTGGG
1 AAAAATAAGCGCCTTCCATCCGGGAAGGGCGTTTTGGG
53079 AAAAA
1 AAAAA
53084 GTTAGTAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 4 0.11
38 34 0.89
ACGTcount: A:0.30, C:0.16, G:0.32, T:0.22
Consensus pattern (38 bp):
AAAAATAAGCGCCTTCCATCCGGGAAGGGCGTTTTGGG
Found at i:53736 original size:12 final size:12
Alignment explanation
Indices: 53716--53746 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
53706 CAATTAACAC
53716 ATAAAAAAAGATA
1 ATAAAAAAA-ATA
53729 ATAAAAAAAATA
1 ATAAAAAAAATA
53741 ATAAAA
1 ATAAAA
53747 GCAAATCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (12 bp):
ATAAAAAAAATA
Found at i:56282 original size:13 final size:13
Alignment explanation
Indices: 56264--56291 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
56254 TTATGCATGA
56264 TGCAATTTATAAG
1 TGCAATTTATAAG
56277 TGCAATTTATAAG
1 TGCAATTTATAAG
56290 TG
1 TG
56292 AAATATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (13 bp):
TGCAATTTATAAG
Found at i:57000 original size:34 final size:34
Alignment explanation
Indices: 56953--57017 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
56943 CTGAGGTCTG
* *
56953 AAACTGAAGAAGA-CTATTCCGTGGTCGACTTGAA
1 AAACTGAAGAAGACCTA-TCCGAGGTCAACTTGAA
56987 AAACT-AAGAAAGACCTATCCGAGGTCAACTT
1 AAACTGAAG-AAGACCTATCCGAGGTCAACTT
57018 TGATAAATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 3 0.11
34 21 0.78
35 3 0.11
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (34 bp):
AAACTGAAGAAGACCTATCCGAGGTCAACTTGAA
Found at i:57069 original size:28 final size:28
Alignment explanation
Indices: 57025--57185 Score: 94
Period size: 28 Copynumber: 5.4 Consensus size: 28
57015 CTTTGATAAA
* *
57025 TGAAATTGAGA-AAGACCCGTCTGAGGTC
1 TGAAATTGA-ATAGGACCAGTCTGAGGTC
*
57053 TGAAATTGAATAGGACCAGTCTGTGGTC
1 TGAAATTGAATAGGACCAGTCTGAGGTC
* * *
57081 GATATTGAAATTGAGA-AAGACCTGTCTAAGGTC
1 -----TGAAATTGA-ATAGGACCAGTCTGAGGTC
*
57114 TGAAATTGAATAGGACCAGTCTGCGG-C
1 TGAAATTGAATAGGACCAGTCTGAGGTC
* * *
57141 CGATATTGAAATCGAGAAAGACCTGTCTGAGGTC
1 TGAAATTG-AAT--AG---GACCAGTCTGAGGTC
57175 TGAAATTGAAT
1 TGAAATTGAAT
57186 GTCTGAGAAA
Statistics
Matches: 101, Mismatches: 17, Indels: 25
0.71 0.12 0.17
Matches are distributed among these distances:
27 9 0.09
28 46 0.46
30 2 0.02
33 36 0.36
34 8 0.08
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (28 bp):
TGAAATTGAATAGGACCAGTCTGAGGTC
Found at i:57120 original size:61 final size:61
Alignment explanation
Indices: 57025--57185 Score: 277
Period size: 61 Copynumber: 2.6 Consensus size: 61
57015 CTTTGATAAA
* * *
57025 TGAAATTGAGAAAGACCCGTCTGAGGTCTGAAATTGAATAGGACCAGTCTGTGGTCGATAT
1 TGAAATTGAGAAAGACCTGTCTGAGGTCTGAAATTGAATAGGACCAGTCTGCGGCCGATAT
*
57086 TGAAATTGAGAAAGACCTGTCTAAGGTCTGAAATTGAATAGGACCAGTCTGCGGCCGATAT
1 TGAAATTGAGAAAGACCTGTCTGAGGTCTGAAATTGAATAGGACCAGTCTGCGGCCGATAT
*
57147 TGAAATCGAGAAAGACCTGTCTGAGGTCTGAAATTGAAT
1 TGAAATTGAGAAAGACCTGTCTGAGGTCTGAAATTGAAT
57186 GTCTGAGAAA
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 94 1.00
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (61 bp):
TGAAATTGAGAAAGACCTGTCTGAGGTCTGAAATTGAATAGGACCAGTCTGCGGCCGATAT
Found at i:57152 original size:33 final size:32
Alignment explanation
Indices: 57053--57152 Score: 84
Period size: 33 Copynumber: 3.2 Consensus size: 32
57043 GTCTGAGGTC
*
57053 TGAAATTGAATAGGACCAGTCTGTGGTCGATAT
1 TGAAATTGAATAGGACCAGTCTGAGG-CGATAT
* * * *
57086 TGAAATTGAGA-AAGACCTGTCT-AAG-G-T-C
1 TGAAATTGA-ATAGGACCAGTCTGAGGCGATAT
*
57114 TGAAATTGAATAGGACCAGTCTGCGGCCGATAT
1 TGAAATTGAATAGGACCAGTCTGAGG-CGATAT
57147 TGAAAT
1 TGAAAT
57153 CGAGAAAGAC
Statistics
Matches: 50, Mismatches: 10, Indels: 14
0.68 0.14 0.19
Matches are distributed among these distances:
27 1 0.02
28 18 0.36
29 2 0.04
30 1 0.02
31 1 0.02
32 2 0.04
33 24 0.48
34 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (32 bp):
TGAAATTGAATAGGACCAGTCTGAGGCGATAT
Found at i:57376 original size:102 final size:102
Alignment explanation
Indices: 57226--57410 Score: 273
Period size: 102 Copynumber: 1.8 Consensus size: 102
57216 TTTGATATTG
* * *
57226 AGAAAGACCTGTCGGAGGTCAACTTTGATAATTGAAATTGAGAGAGACCTATATGAGGTATGGAA
1 AGAAAGACCTGTCGGAGGTCAACTTTGATAAATGAAATTGAGAAAGACCCATATGAGGTATGGAA
57291 TTGAAGAAGACCAGTCTGTGGTCGATATGAAAAACTA
66 TTGAAGAAGACCAGTCTGTGGTCGATATGAAAAACTA
* * * *
57328 AGAAAGACCTCTTC-GAGGTCAACTTTGATAAATGAAATTGAGAAAGACCCGTCTGAGGTCTGGA
1 AGAAAGACCT-GTCGGAGGTCAACTTTGATAAATGAAATTGAGAAAGACCCATATGAGGTATGGA
* *
57392 ATTGAATAAGACTAGTCTG
65 ATTGAAGAAGACCAGTCTG
57411 AGTCTGTGGT
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
102 71 0.97
103 2 0.03
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (102 bp):
AGAAAGACCTGTCGGAGGTCAACTTTGATAAATGAAATTGAGAAAGACCCATATGAGGTATGGAA
TTGAAGAAGACCAGTCTGTGGTCGATATGAAAAACTA
Found at i:57403 original size:28 final size:27
Alignment explanation
Indices: 57363--57416 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
57353 TGATAAATGA
*
57363 AATTGAGAAAGACCCGTCTGAGGTCTGG
1 AATTGAGAAAGACCAGTCTGA-GTCTGG
*
57391 AATTGA-ATAAGACTAGTCTGAGTCTG
1 AATTGAGA-AAGACCAGTCTGAGTCTG
57417 TGGTTGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (27 bp):
AATTGAGAAAGACCAGTCTGAGTCTGG
Found at i:57449 original size:33 final size:31
Alignment explanation
Indices: 57412--57636 Score: 125
Period size: 33 Copynumber: 7.3 Consensus size: 31
57402 ACTAGTCTGA
* *
57412 GTCTGTGGTTGATATTGAAATTGGGAAAGACCT
1 GTCTGAGGTCGATATTGAAA-T-GGAAAGACCT
* * *
57445 GTCTGAGGTCTGAAATTG-AAT---AGGACCA
1 GTCTGAGGTC-GATATTGAAATGGAAAGACCT
* *
57473 GTCTGTGGTCGATATTGAAACTGAGAAAGACTT
1 GTCTGAGGTCGATATTGAAA-TG-GAAAGACCT
* *
57506 GTCTGAGGTCAACT-TTG-AA--G-AAGACCA
1 GTCTGAGGTCGA-TATTGAAATGGAAAGACCT
*
57533 GTCTGTGGTCGATATTGAAATTGAGAAAGACCT
1 GTCTGAGGTCGATATTGAAA-TG-GAAAGACCT
* * *
57566 GTCTGAGGTCTGAAATTG-AA--G-ACGACCA
1 GTCTGAGGTC-GATATTGAAATGGAAAGACCT
* *
57594 GTCTGTGGTCGATACTGAAACTGAGAAAGACCT
1 GTCTGAGGTCGATATTGAAA-TG-GAAAGACCT
57627 GTCTGAGGTC
1 GTCTGAGGTC
57637 AACTTTGAAG
Statistics
Matches: 143, Mismatches: 27, Indels: 44
0.67 0.13 0.21
Matches are distributed among these distances:
26 1 0.01
27 29 0.20
28 35 0.24
29 2 0.01
32 5 0.03
33 58 0.41
34 13 0.09
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (31 bp):
GTCTGAGGTCGATATTGAAATGGAAAGACCT
Found at i:57481 original size:61 final size:61
Alignment explanation
Indices: 57360--57636 Score: 360
Period size: 61 Copynumber: 4.5 Consensus size: 61
57350 CTTTGATAAA
* * * *
57360 TGAAATTGAGAAAGACCCGTCTGAGGTCTGGAATTGAATAAGACTAGTCTGAGTCTGTGGTTGAT
1 TGAAATTGAGAAAGACCTGTCTGAGGTCTGAAATTGAAGAAGAC----C--AGTCTGTGGTCGAT
57425 AT
60 AT
* * *
57427 TGAAATTGGGAAAGACCTGTCTGAGGTCTGAAATTGAATAGGACCAGTCTGTGGTCGATAT
1 TGAAATTGAGAAAGACCTGTCTGAGGTCTGAAATTGAAGAAGACCAGTCTGTGGTCGATAT
* * *
57488 TGAAACTGAGAAAGACTTGTCTGAGGTC--AACTTTGAAGAAGACCAGTCTGTGGTCGATAT
1 TGAAATTGAGAAAGACCTGTCTGAGGTCTGAA-ATTGAAGAAGACCAGTCTGTGGTCGATAT
* *
57548 TGAAATTGAGAAAGACCTGTCTGAGGTCTGAAATTGAAGACGACCAGTCTGTGGTCGATAC
1 TGAAATTGAGAAAGACCTGTCTGAGGTCTGAAATTGAAGAAGACCAGTCTGTGGTCGATAT
*
57609 TGAAACTGAGAAAGACCTGTCTGAGGTC
1 TGAAATTGAGAAAGACCTGTCTGAGGTC
57637 AACTTTGAAG
Statistics
Matches: 190, Mismatches: 17, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
59 2 0.01
60 52 0.27
61 93 0.49
62 2 0.01
63 1 0.01
67 40 0.21
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27
Consensus pattern (61 bp):
TGAAATTGAGAAAGACCTGTCTGAGGTCTGAAATTGAAGAAGACCAGTCTGTGGTCGATAT
Found at i:57581 original size:121 final size:121
Alignment explanation
Indices: 57411--57647 Score: 420
Period size: 121 Copynumber: 2.0 Consensus size: 121
57401 GACTAGTCTG
* * * *
57411 AGTCTGTGGTTGATATTGAAATTGGGAAAGACCTGTCTGAGGTCTGAAATTGAATAGGACCAGTC
1 AGTCTGTGGTCGATATTGAAATTGAGAAAGACCTGTCTGAGGTCTGAAATTGAAGACGACCAGTC
* *
57476 TGTGGTCGATATTGAAACTGAGAAAGACTTGTCTGAGGTCAACTTTGAAGAAGACC
66 TGTGGTCGATACTGAAACTGAGAAAGACCTGTCTGAGGTCAACTTTGAAGAAGACC
57532 AGTCTGTGGTCGATATTGAAATTGAGAAAGACCTGTCTGAGGTCTGAAATTGAAGACGACCAGTC
1 AGTCTGTGGTCGATATTGAAATTGAGAAAGACCTGTCTGAGGTCTGAAATTGAAGACGACCAGTC
57597 TGTGGTCGATACTGAAACTGAGAAAGACCTGTCTGAGGTCAACTTTGAAGA
66 TGTGGTCGATACTGAAACTGAGAAAGACCTGTCTGAGGTCAACTTTGAAGA
57648 GAAACTGACA
Statistics
Matches: 110, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
121 110 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27
Consensus pattern (121 bp):
AGTCTGTGGTCGATATTGAAATTGAGAAAGACCTGTCTGAGGTCTGAAATTGAAGACGACCAGTC
TGTGGTCGATACTGAAACTGAGAAAGACCTGTCTGAGGTCAACTTTGAAGAAGACC
Found at i:57728 original size:47 final size:47
Alignment explanation
Indices: 57670--57776 Score: 144
Period size: 47 Copynumber: 2.3 Consensus size: 47
57660 GCTGAAGGAA
*
57670 ACCAACTGTGGTCACCAAATTGTAGAC-TCGCATGGAAGCGAGAAAAG
1 ACCAACTGTGGTCACCAAATTGTA-ACTTCGCATAGAAGCGAGAAAAG
* * **
57717 ACCGACTGTGGTCACCAAATTGTAACTTTGCATAGAATTGAGAAAAG
1 ACCAACTGTGGTCACCAAATTGTAACTTCGCATAGAAGCGAGAAAAG
*
57764 ACCAACTCTGGTC
1 ACCAACTGTGGTC
57777 GAAGGACCGC
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
46 2 0.04
47 50 0.96
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.21
Consensus pattern (47 bp):
ACCAACTGTGGTCACCAAATTGTAACTTCGCATAGAAGCGAGAAAAG
Found at i:57838 original size:48 final size:48
Alignment explanation
Indices: 57755--58277 Score: 707
Period size: 48 Copynumber: 11.0 Consensus size: 48
57745 TGCATAGAAT
* ***
57755 TGAGAAAAGACCAACTCT-GGTC-GAAGGACCGCTGACTCACATGGAAG
1 TGAGGAAAGACCAACT-TGGGTCGGAAGGATTTCTGACTCACATGGAAG
* *
57802 TGAGGAAACACCAACTTGGGTGGGAAGGATTTCTGACTCACATGGAAG
1 TGAGGAAAGACCAACTTGGGTCGGAAGGATTTCTGACTCACATGGAAG
* * * *
57850 TGTGGAAAGACCAACTTGGGTCGGAAGGATTACCGGCTCACATGGAAG
1 TGAGGAAAGACCAACTTGGGTCGGAAGGATTTCTGACTCACATGGAAG
*
57898 TGAGGAAAGACCAACTTGGGTC-GAAGGATTTTTGACTCACATGGAAG
1 TGAGGAAAGACCAACTTGGGTCGGAAGGATTTCTGACTCACATGGAAG
* *
57945 TGAGGAAAGACCAACTTGGGTCGAAACGATTTCTGACTCACATGGAAG
1 TGAGGAAAGACCAACTTGGGTCGGAAGGATTTCTGACTCACATGGAAG
*
57993 TGATGAAAGACCAACTTGGGTC-GAAGGATTTCTGACTCACATGGAAG
1 TGAGGAAAGACCAACTTGGGTCGGAAGGATTTCTGACTCACATGGAAG
* * *
58040 TGAGGAAAGACCAACTTGGGTCGAAATGACTTCTGACTCACATGGAAG
1 TGAGGAAAGACCAACTTGGGTCGGAAGGATTTCTGACTCACATGGAAG
** ** *
58088 TGAGGAAAGACCAACTTGGGTCAAAACAATTTCTAACTCACATGGAAG
1 TGAGGAAAGACCAACTTGGGTCGGAAGGATTTCTGACTCACATGGAAG
* *
58136 TGAGAAAAGACCAACTTGGGTC-GAAGGATTACTGACTCACATGGAAG
1 TGAGGAAAGACCAACTTGGGTCGGAAGGATTTCTGACTCACATGGAAG
* *
58183 TGAGGAAAGACCAACTTGGGTCGG-AGGATTACTAACTCACATGGAAG
1 TGAGGAAAGACCAACTTGGGTCGGAAGGATTTCTGACTCACATGGAAG
* * * * * *
58230 TAAGGAAAGACCAACTTGGGTCGAAAAGATTACTGGCTCACAGGGAAG
1 TGAGGAAAGACCAACTTGGGTCGGAAGGATTTCTGACTCACATGGAAG
58278 CAAGGTTGAC
Statistics
Matches: 424, Mismatches: 46, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
46 1 0.00
47 189 0.45
48 234 0.55
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (48 bp):
TGAGGAAAGACCAACTTGGGTCGGAAGGATTTCTGACTCACATGGAAG
Found at i:57940 original size:95 final size:95
Alignment explanation
Indices: 57755--58277 Score: 739
Period size: 95 Copynumber: 5.5 Consensus size: 95
57745 TGCATAGAAT
* *** *
57755 TGAGAAAAGACCAACTCT-GGTCG-AAGGACCGCTGACTCACATGGAAGTGAGGAAACACCAACT
1 TGAGGAAAGACCAACT-TGGGTCGAAAGGATTACTGACTCACATGGAAGTGAGGAAAGACCAACT
*
57818 TGGGTGGGAAGGATTTCTGACTCACATGGAAG
65 TGGGT-CGAAGGATTTCTGACTCACATGGAAG
* * * *
57850 TGTGGAAAGACCAACTTGGGTCGGAAGGATTACCGGCTCACATGGAAGTGAGGAAAGACCAACTT
1 TGAGGAAAGACCAACTTGGGTCGAAAGGATTACTGACTCACATGGAAGTGAGGAAAGACCAACTT
*
57915 GGGTCGAAGGATTTTTGACTCACATGGAAG
66 GGGTCGAAGGATTTCTGACTCACATGGAAG
* * *
57945 TGAGGAAAGACCAACTTGGGTCGAAACGATTTCTGACTCACATGGAAGTGATGAAAGACCAACTT
1 TGAGGAAAGACCAACTTGGGTCGAAAGGATTACTGACTCACATGGAAGTGAGGAAAGACCAACTT
58010 GGGTCGAAGGATTTCTGACTCACATGGAAG
66 GGGTCGAAGGATTTCTGACTCACATGGAAG
*
58040 TGAGGAAAGACCAACTTGGGTCGAAATGACTT-CTGACTCACATGGAAGTGAGGAAAGACCAACT
1 TGAGGAAAGACCAACTTGGGTCGAAAGGA-TTACTGACTCACATGGAAGTGAGGAAAGACCAACT
* ** *
58104 TGGGTCAAAACAATTTCTAACTCACATGGAAG
65 TGGGTC-GAAGGATTTCTGACTCACATGGAAG
*
58136 TGAGAAAAGACCAACTTGGGTCG-AAGGATTACTGACTCACATGGAAGTGAGGAAAGACCAACTT
1 TGAGGAAAGACCAACTTGGGTCGAAAGGATTACTGACTCACATGGAAGTGAGGAAAGACCAACTT
* * *
58200 GGGTCGGAGGATTACTAACTCACATGGAAG
66 GGGTCGAAGGATTTCTGACTCACATGGAAG
* * * *
58230 TAAGGAAAGACCAACTTGGGTCGAAAAGATTACTGGCTCACAGGGAAG
1 TGAGGAAAGACCAACTTGGGTCGAAAGGATTACTGACTCACATGGAAG
58278 CAAGGTTGAC
Statistics
Matches: 386, Mismatches: 36, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
94 44 0.11
95 258 0.67
96 84 0.22
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (95 bp):
TGAGGAAAGACCAACTTGGGTCGAAAGGATTACTGACTCACATGGAAGTGAGGAAAGACCAACTT
GGGTCGAAGGATTTCTGACTCACATGGAAG
Found at i:57951 original size:143 final size:142
Alignment explanation
Indices: 57755--58277 Score: 755
Period size: 143 Copynumber: 3.7 Consensus size: 142
57745 TGCATAGAAT
* ** *
57755 TGAGAAAAGACCAACTCT-GGTCGAAGGACCGCTGACTCACATGGAAGTGAGGAAACACCAACTT
1 TGAGGAAAGACCAACT-TGGGTCGAAGGACTTCTGACTCACATGGAAGTGAGGAAAGACCAACTT
* * * *
57819 GGGTGGGAAGGATTTCTGACTCACATGGAAGTGTGGAAAGACCAACTTGGGTCGGAAGGATTACC
65 GGGTCGAAACGATTTCTGACTCACATGGAAGTGTGGAAAGACCAACTTGGGTC-GAAGGATTACT
*
57884 GGCTCACATGGAAG
129 GACTCACATGGAAG
* *
57898 TGAGGAAAGACCAACTTGGGTCGAAGGATTTTTGACTCACATGGAAGTGAGGAAAGACCAACTTG
1 TGAGGAAAGACCAACTTGGGTCGAAGGACTTCTGACTCACATGGAAGTGAGGAAAGACCAACTTG
*
57963 GGTCGAAACGATTTCTGACTCACATGGAAGTGAT-GAAAGACCAACTTGGGTCGAAGGATTTCTG
66 GGTCGAAACGATTTCTGACTCACATGGAAGTG-TGGAAAGACCAACTTGGGTCGAAGGATTACTG
58027 ACTCACATGGAAG
130 ACTCACATGGAAG
*
58040 TGAGGAAAGACCAACTTGGGTCGAAATGACTTCTGACTCACATGGAAGTGAGGAAAGACCAACTT
1 TGAGGAAAGACCAACTTGGGTCG-AAGGACTTCTGACTCACATGGAAGTGAGGAAAGACCAACTT
* * * * *
58105 GGGTCAAAACAATTTCTAACTCACATGGAAGTGAGAAAAGACCAACTTGGGTCGAAGGATTACTG
65 GGGTCGAAACGATTTCTGACTCACATGGAAGTGTGGAAAGACCAACTTGGGTCGAAGGATTACTG
58170 ACTCACATGGAAG
130 ACTCACATGGAAG
* * *
58183 TGAGGAAAGACCAACTTGGGTCGGAGGA-TTACTAACTCACATGGAAGTAAGGAAAGACCAACTT
1 TGAGGAAAGACCAACTTGGGTCGAAGGACTT-CTGACTCACATGGAAGTGAGGAAAGACCAACTT
* * * *
58247 GGGTCGAAAAGATTACTGGCTCACAGGGAAG
65 GGGTCGAAACGATTTCTGACTCACATGGAAG
58278 CAAGGTTGAC
Statistics
Matches: 343, Mismatches: 32, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
141 2 0.01
142 104 0.30
143 236 0.69
144 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (142 bp):
TGAGGAAAGACCAACTTGGGTCGAAGGACTTCTGACTCACATGGAAGTGAGGAAAGACCAACTTG
GGTCGAAACGATTTCTGACTCACATGGAAGTGTGGAAAGACCAACTTGGGTCGAAGGATTACTGA
CTCACATGGAAG
Found at i:58410 original size:68 final size:68
Alignment explanation
Indices: 58327--58509 Score: 294
Period size: 68 Copynumber: 2.6 Consensus size: 68
58317 AACTGAGGCT
*
58327 TAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAA
1 TAAACTTACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAA
58392 AGC
66 AGC
58395 TAAACTTACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAA
1 TAAACTTACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAA
*
58460 GGC
66 AGC
* *
58463 TAAACTAACTGACTCGTATGGAAACGAGTTTCGCATGTGGAAAAGCC
1 TAAACT---T-ACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
58510 AAGGCATTCG
Statistics
Matches: 107, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
68 72 0.67
71 1 0.01
72 34 0.32
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (68 bp):
TAAACTTACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAA
AGC
Found at i:59494 original size:16 final size:17
Alignment explanation
Indices: 59452--59494 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
59442 GCCTCTTTTC
*
59452 TTCATTCTTTTTTCTTT
1 TTCATTCTTTTTTCCTT
59469 TTC-TTCTTTTTTCCTT
1 TTCATTCTTTTTTCCTT
59485 TTCATT-TTTT
1 TTCATTCTTTT
59495 CTTTCATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 19 0.79
17 5 0.21
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.77
Consensus pattern (17 bp):
TTCATTCTTTTTTCCTT
Found at i:59499 original size:12 final size:12
Alignment explanation
Indices: 59447--59506 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
59437 CTAGAGCCTC
59447 TTTTC-TTCATT
1 TTTTCTTTCATT
*
59458 CTTT-TTTC--T
1 TTTTCTTTCATT
59467 TTTTC-TTC-TT
1 TTTTCTTTCATT
59477 TTTTCCTTTTCATT
1 TTTT-C-TTTCATT
59491 TTTTCTTTCATT
1 TTTTCTTTCATT
59503 TTTT
1 TTTT
59507 ACATGCACTT
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
9 7 0.17
10 5 0.12
11 7 0.17
12 11 0.28
13 4 0.10
14 6 0.15
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTCTTTCATT
Found at i:60234 original size:45 final size:45
Alignment explanation
Indices: 60180--60279 Score: 155
Period size: 45 Copynumber: 2.2 Consensus size: 45
60170 AAAACACAAC
* * *
60180 TTTGGAAAACCATTTTATCAAAACCTCTTGAAAACCATGACTGTT
1 TTTGAAAAACCATTTTATCAAAACCTCTTGAAAACCATAACTCTT
* *
60225 TTTGAAAAACCATTTTATCAAAACCTTTTGAAAAGCATAACTCTT
1 TTTGAAAAACCATTTTATCAAAACCTCTTGAAAACCATAACTCTT
60270 TTTGAAAAAC
1 TTTGAAAAAC
60280 ATCGTTGCTT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (45 bp):
TTTGAAAAACCATTTTATCAAAACCTCTTGAAAACCATAACTCTT
Found at i:60309 original size:10 final size:10
Alignment explanation
Indices: 60288--60322 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
60278 ACATCGTTGC
60288 TTTTTCTCTT
1 TTTTTCTCTT
60298 TTTCTT-TCTT
1 TTT-TTCTCTT
60308 TTTTTCTCTT
1 TTTTTCTCTT
60318 TTTTT
1 TTTTT
60323 TATCGGGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.09
10 19 0.83
11 2 0.09
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTCTCTT
Found at i:62562 original size:16 final size:17
Alignment explanation
Indices: 62543--62575 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
62533 AATGTGATGG
62543 TGAATGAATG-AACAAA
1 TGAATGAATGAAACAAA
*
62559 TGAATGCATGAAACAAA
1 TGAATGAATGAAACAAA
62576 AAAAATGGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.55, C:0.09, G:0.18, T:0.18
Consensus pattern (17 bp):
TGAATGAATGAAACAAA
Found at i:65286 original size:62 final size:63
Alignment explanation
Indices: 65164--65588 Score: 296
Period size: 62 Copynumber: 6.6 Consensus size: 63
65154 TGCAAGAACA
* * * *
65164 TGACAAAATTGACCCTTTGTCCGAAAGGGTATTTTGGGAA-ATAGAAACTATAT-AAGAGAATG
1 TGACGAAACTGACCCTTTGTCCGAAAGGGTATTTTGGGAATCTAGAAACTAAATGAA-AGAATG
* * * * *
65226 TGACGAAACTGACCCTTTGTCTGAAAAGGTATTTTGGGAA-CTATAATCTAAGTGAAAGAATG
1 TGACGAAACTGACCCTTTGTCCGAAAGGGTATTTTGGGAATCTAGAAACTAAATGAAAGAATG
* * * * *
65288 TGGA-GAAACTGACCATTTGTCTGAAAGAGTATTTTGGGAATGCT--AAACTCAAATGCAGGAAT
1 T-GACGAAACTGACCCTTTGTCCGAAAGGGTATTTTGGGAAT-CTAGAAACT-AAATGAAAGAAT
65350 G
63 G
* * * * *
65351 TGATGAAACT-AGCTCTTTGTCCGAAAGGGCT-TTTTGGGAAACCTTGAAACTAAATGCAAGAAT
1 TGACGAAACTGA-CCCTTTGTCCGAAAGGG-TATTTTGGG-AATCTAGAAACTAAATGAAAGAAT
65414 G
63 G
* * * * * *
65415 TGA-GAAAACTAACCCTTTGTCCGAAAGGTTATTTTTGGGAATCGAAAATACTTAACTTAAATGC
1 TGACG-AAACTGACCCTTTGTCCGAAAGGGTA-TTTTGGGAATCTAGAA-AC-TAAATGAAA---
65479 GGGAATG
59 --GAATG
* * * * * * * *
65486 TGAC-AAAATTAGCCCTTTGTCTGAAAGGGCATTTTGGGAAAACTAGAACCTAAATGCAAGAAAG
1 TGACGAAACTGA-CCCTTTGTCCGAAAGGGTATTTTGGG-AATCTAGAAACTAAATGAAAGAATG
* *
65550 TGAC-AAATTGACCCTTTGTCCGAAAGGGTATTCTGGGAA
1 TGACGAAACTGACCCTTTGTCCGAAAGGGTATTTTGGGAA
65589 AAAGCAAGTA
Statistics
Matches: 289, Mismatches: 49, Indels: 50
0.74 0.13 0.13
Matches are distributed among these distances:
62 93 0.32
63 68 0.24
64 58 0.20
65 15 0.05
66 6 0.02
69 6 0.02
70 13 0.04
71 30 0.10
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (63 bp):
TGACGAAACTGACCCTTTGTCCGAAAGGGTATTTTGGGAATCTAGAAACTAAATGAAAGAATG
Found at i:65521 original size:135 final size:134
Alignment explanation
Indices: 65333--65581 Score: 345
Period size: 135 Copynumber: 1.9 Consensus size: 134
65323 GGGAATGCTA
** * * * *
65333 AACTCAAATGCAGGAATGTGATGAAACTAGCTCTTTGTCCGAAAGGGCTTTTTGGGAAACCTTGA
1 AACTCAAATGCAGGAATGTGACAAAACTAGCCCTTTGTCCGAAAGGGCATTTTGGGAAAACTAGA
* *
65398 AACTAAATGCAAGAATGTGAGAAAACTAACCCTTTGTCCGAAAGGTTATTTTTGGGAATCGAAAA
66 AACTAAATGCAAGAAAGTGA-AAAACTAACCCTTTGTCCGAAAGGGTATTTTTGGGAATCGAAAA
65463 TACTT
130 TACTT
* * * *
65468 AACTTAAATGCGGGAATGTGACAAAATTAGCCCTTTGTCTGAAAGGGCATTTTGGGAAAACTAGA
1 AACTCAAATGCAGGAATGTGACAAAACTAGCCCTTTGTCCGAAAGGGCATTTTGGGAAAACTAGA
* * * *
65533 ACCTAAATGCAAGAAAGTGACAAATTGACCCTTTGTCCGAAAGGGTATT
66 AACTAAATGCAAGAAAGTGAAAAACTAACCCTTTGTCCGAAAGGGTATT
65582 CTGGGAAAAA
Statistics
Matches: 98, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
134 25 0.26
135 73 0.74
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (134 bp):
AACTCAAATGCAGGAATGTGACAAAACTAGCCCTTTGTCCGAAAGGGCATTTTGGGAAAACTAGA
AACTAAATGCAAGAAAGTGAAAAACTAACCCTTTGTCCGAAAGGGTATTTTTGGGAATCGAAAAT
ACTT
Found at i:65640 original size:38 final size:38
Alignment explanation
Indices: 65598--65678 Score: 110
Period size: 38 Copynumber: 2.1 Consensus size: 38
65588 AAAAGCAAGT
* *
65598 AAAAATAGGCGCCTTTCGA-CCGGGAAGGGCATTTTGGG
1 AAAAATAAGCGCC-TTCCATCCGGGAAGGGCATTTTGGG
* *
65636 AAAAATAAGTGCCTTCCATCTGGGAAGGGCATTTTGGG
1 AAAAATAAGCGCCTTCCATCCGGGAAGGGCATTTTGGG
65674 AAAAA
1 AAAAA
65679 GTTAGTAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 4 0.11
38 34 0.89
ACGTcount: A:0.32, C:0.16, G:0.30, T:0.22
Consensus pattern (38 bp):
AAAAATAAGCGCCTTCCATCCGGGAAGGGCATTTTGGG
Found at i:65736 original size:49 final size:49
Alignment explanation
Indices: 65636--65736 Score: 132
Period size: 49 Copynumber: 2.1 Consensus size: 49
65626 GCATTTTGGG
** * *
65636 AAAAATAAGTGCCTTCCATCTGGGAAGGGCATTTTGGGAAAAAGTTAGT
1 AAAAATAAACGCCTTCCATCTAGGAAGGGCATTTTGGGAAAAAGTCAGT
* *
65685 AAAAATAAACGCCTTCCATCTAGGATGGGCGTTTTGGGAAAAAG-CAGGT
1 AAAAATAAACGCCTTCCATCTAGGAAGGGCATTTTGGGAAAAAGTCA-GT
65734 AAA
1 AAA
65737 GACTGAAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 1 0.02
49 44 0.98
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.24
Consensus pattern (49 bp):
AAAAATAAACGCCTTCCATCTAGGAAGGGCATTTTGGGAAAAAGTCAGT
Found at i:72890 original size:37 final size:37
Alignment explanation
Indices: 72760--72911 Score: 211
Period size: 36 Copynumber: 4.2 Consensus size: 37
72750 TTTTTTTAAG
** *
72760 ATTAAGT-TCTTTATTGATTCCACTTAATTACCCTGA
1 ATTAAGTCTCTTTATTGACGCTACTTAATTACCCTGA
* *
72796 ATTAAG-CTCTTTATTGACCCAACTTAATTACCCTGA
1 ATTAAGTCTCTTTATTGACGCTACTTAATTACCCTGA
*
72832 ATTAAGT-TCTTTATTGACGCTACTTAATTACACTGA
1 ATTAAGTCTCTTTATTGACGCTACTTAATTACCCTGA
* *
72868 AGTAAGTCCCTTTATTGACGCTACTTAATTACCCTGA
1 ATTAAGTCTCTTTATTGACGCTACTTAATTACCCTGA
72905 ATTAAGT
1 ATTAAGT
72912 TCCTAACTTG
Statistics
Matches: 103, Mismatches: 10, Indels: 5
0.87 0.08 0.04
Matches are distributed among these distances:
36 70 0.68
37 33 0.32
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (37 bp):
ATTAAGTCTCTTTATTGACGCTACTTAATTACCCTGA
Found at i:72935 original size:32 final size:32
Alignment explanation
Indices: 72890--72961 Score: 110
Period size: 32 Copynumber: 2.2 Consensus size: 32
72880 TATTGACGCT
72890 ACTTAATTACCCTGAATTAAGT-TCCTAACTTG
1 ACTTAATTACCCTGAATTAAGTCT-CTAACTTG
* *
72922 ACTTAATTGCCCTGAATTAAGTCTCTGACTTG
1 ACTTAATTACCCTGAATTAAGTCTCTAACTTG
72954 ACTTAATT
1 ACTTAATT
72962 TCCTTCCTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 36 0.97
33 1 0.03
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (32 bp):
ACTTAATTACCCTGAATTAAGTCTCTAACTTG
Found at i:72977 original size:69 final size:63
Alignment explanation
Indices: 72904--73071 Score: 187
Period size: 69 Copynumber: 2.5 Consensus size: 63
72894 AATTACCCTG
*
72904 AATTAAGTTCC-TAACT-TGACTTAATTGCCCTGAATTAAGTCTCTGACTTGACTTAATTTCCTT
1 AATTAAG-TCCTTAACTCT-ACTTAATT-CCCTGAATCAAGTC-CT--C-T-ACTTAATTTCCTT
72967 CCTTGA
58 CCTTGA
72973 AATTAAGTCCTTAACTCTACTTAATTCCCCTCCTTTGAATCAAGTCCTCTACTTAATTTCCTTCC
1 AATTAAGTCCTTAACTCTACTTAATT---C-CC--TGAATCAAGTCCTCTACTTAATTTCCTTCC
73038 TTGA
60 TTGA
73042 AATTAAGTCCTTAACTCTACTTAATTCCCT
1 AATTAAGTCCTTAACTCTACTTAATTCCCT
73072 TCCTTGATCT
Statistics
Matches: 90, Mismatches: 2, Indels: 20
0.80 0.02 0.18
Matches are distributed among these distances:
63 1 0.01
65 2 0.02
66 1 0.01
68 3 0.03
69 65 0.72
70 2 0.02
71 2 0.02
72 2 0.02
73 2 0.02
74 10 0.11
ACGTcount: A:0.26, C:0.26, G:0.08, T:0.40
Consensus pattern (63 bp):
AATTAAGTCCTTAACTCTACTTAATTCCCTGAATCAAGTCCTCTACTTAATTTCCTTCCTTGA
Found at i:72995 original size:37 final size:37
Alignment explanation
Indices: 72954--73078 Score: 163
Period size: 37 Copynumber: 3.5 Consensus size: 37
72944 CTCTGACTTG
*
72954 ACTTAATTTCCTTCCTTGAAATTAAGTCCTTAACTCT
1 ACTTAATTCCCTTCCTTGAAATTAAGTCCTTAACTCT
* *
72991 ACTTAATTCCCCTCCTTTG-AATCAAGT-C----CTCT
1 ACTTAATTCCCTTCC-TTGAAATTAAGTCCTTAACTCT
*
73023 ACTTAATTTCCTTCCTTGAAATTAAGTCCTTAACTCT
1 ACTTAATTCCCTTCCTTGAAATTAAGTCCTTAACTCT
73060 ACTTAATTCCCTTCCTTGA
1 ACTTAATTCCCTTCCTTGA
73079 TCTTAATCTT
Statistics
Matches: 74, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
31 3 0.04
32 24 0.32
33 1 0.01
36 1 0.01
37 42 0.57
38 3 0.04
ACGTcount: A:0.25, C:0.28, G:0.06, T:0.42
Consensus pattern (37 bp):
ACTTAATTCCCTTCCTTGAAATTAAGTCCTTAACTCT
Found at i:73028 original size:32 final size:32
Alignment explanation
Indices: 72987--73052 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
72977 AAGTCCTTAA
72987 CTCTACTTAATTCCCCTCCTTTG-AATCAAGTC
1 CTCTACTTAATTCCCCTCC-TTGAAATCAAGTC
* * *
73019 CTCTACTTAATTTCCTTCCTTGAAATTAAGTC
1 CTCTACTTAATTCCCCTCCTTGAAATCAAGTC
73051 CT
1 CT
73053 TAACTCTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 3 0.10
32 27 0.90
ACGTcount: A:0.23, C:0.30, G:0.06, T:0.41
Consensus pattern (32 bp):
CTCTACTTAATTCCCCTCCTTGAAATCAAGTC
Found at i:78179 original size:35 final size:36
Alignment explanation
Indices: 78134--78441 Score: 272
Period size: 35 Copynumber: 8.6 Consensus size: 36
78124 TTAAGTCGAT
78134 CTTAATTACCCTGAATTAAGTTAAC-TACTGACTCA
1 CTTAATTACCCTGAATTAAGTTAACTTACTGACTCA
* * * * * **
78169 CTTGACTACCCCGAATTAAGTT-ACTTATTAACTTG
1 CTTAATTACCCTGAATTAAGTTAACTTACTGACTCA
* *
78204 CTTGATTACCCTGAATTAAGTT-ACTTATTGACTCA
1 CTTAATTACCCTGAATTAAGTTAACTTACTGACTCA
* * *
78239 CTTAATTACCCTGAATTAAGTTATTTA-TTGCTGATTTA
1 CTTAATTACCCTGAATTAAGTTA---ACTTACTGACTCA
* **
78277 CTTAATTACCCTGAATTAAGTTATC-TACCT-ACTTG
1 CTTAATTACCCTGAATTAAGTTAACTTA-CTGACTCA
*
78312 CTTAATTACCCTGAATTAAGTT-ACTTATTGACTCA
1 CTTAATTACCCTGAATTAAGTTAACTTACTGACTCA
** * * * *
78347 CTTAATTACCCTGAATTAAGTTATTTTTTGCTAATTTA
1 CTTAATTACCCTGAATTAAGTTA--ACTTACTGACTCA
* * **
78385 CTTAATTACCCTGAATTAAGTTATC-TACCGACTTG
1 CTTAATTACCCTGAATTAAGTTAACTTACTGACTCA
78420 CTTAATTACCCTGAATTAAGTT
1 CTTAATTACCCTGAATTAAGTT
78442 GCTTATTACT
Statistics
Matches: 223, Mismatches: 38, Indels: 24
0.78 0.13 0.08
Matches are distributed among these distances:
34 4 0.02
35 156 0.70
36 3 0.01
38 59 0.26
39 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (36 bp):
CTTAATTACCCTGAATTAAGTTAACTTACTGACTCA
Found at i:78225 original size:70 final size:70
Alignment explanation
Indices: 78134--78441 Score: 316
Period size: 73 Copynumber: 4.3 Consensus size: 70
78124 TTAAGTCGAT
* * * *
78134 CTTAATTACCCTGAATTAAGTTAACTACTGACTCACTTGACTACCCCGAATTAAGTTACTTATTA
1 CTTAATTACCCTGAATTAAGTTAACTACTGACTCACTTAATTACCCTGAATTAAGTTACTTATTG
*
78199 ACTTG
66 ACTTA
* * *
78204 CTTGATTACCCTGAATTAAGTT-ACTTATTGACTCACTTAATTACCCTGAATTAAGTTATTTATT
1 CTTAATTACCCTGAATTAAGTTAAC-TACTGACTCACTTAATTACCCTGAATTAAGTTACTTA-T
*
78268 GCTGATTTA
64 --TGACTTA
* **
78277 CTTAATTACCCTGAATTAAGTTATCTACCT-ACTTGCTTAATTACCCTGAATTAAGTTACTTATT
1 CTTAATTACCCTGAATTAAGTTAACTA-CTGACTCACTTAATTACCCTGAATTAAGTTACTTATT
*
78341 GACTCA
65 GACTTA
** * * * *
78347 CTTAATTACCCTGAATTAAGTTATTTTTTGCTAATTTACTTAATTACCCTGAATTAAGTTA-TCT
1 CTTAATTACCCTGAATTAAGTTA---ACTACTGACTCACTTAATTACCCTGAATTAAGTTACT-T
** *
78411 ACCGACTTG
62 ATTGACTTA
78420 CTTAATTACCCTGAATTAAGTT
1 CTTAATTACCCTGAATTAAGTT
78442 GCTTATTACT
Statistics
Matches: 202, Mismatches: 25, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
69 2 0.01
70 81 0.40
71 1 0.00
72 4 0.02
73 112 0.55
74 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (70 bp):
CTTAATTACCCTGAATTAAGTTAACTACTGACTCACTTAATTACCCTGAATTAAGTTACTTATTG
ACTTA
Found at i:78320 original size:108 final size:108
Alignment explanation
Indices: 78134--78448 Score: 460
Period size: 108 Copynumber: 2.9 Consensus size: 108
78124 TTAAGTCGAT
* * * * * * *
78134 CTTAATTACCCTGAATTAAGTTA---ACTACTGACTCACTTGACTACCCCGAATTAAGTTA-CTT
1 CTTAATTACCCTGAATTAAGTTATTTATTGCTGATTTACTTAATTACCCTGAATTAAGTTATC-T
* *
78195 A-TTAACTTGCTTGATTACCCTGAATTAAGTTACTTATTGACTCA
65 ACCT-ACTTGCTTAATTACCCTGAATTAAGTTACTTATTGACTCA
78239 CTTAATTACCCTGAATTAAGTTATTTATTGCTGATTTACTTAATTACCCTGAATTAAGTTATCTA
1 CTTAATTACCCTGAATTAAGTTATTTATTGCTGATTTACTTAATTACCCTGAATTAAGTTATCTA
78304 CCTACTTGCTTAATTACCCTGAATTAAGTTACTTATTGACTCA
66 CCTACTTGCTTAATTACCCTGAATTAAGTTACTTATTGACTCA
* *
78347 CTTAATTACCCTGAATTAAGTTATTTTTTGCTAATTTACTTAATTACCCTGAATTAAGTTATCTA
1 CTTAATTACCCTGAATTAAGTTATTTATTGCTGATTTACTTAATTACCCTGAATTAAGTTATCTA
* *
78412 CCGACTTGCTTAATTACCCTGAATTAAGTTGCTTATT
66 CCTACTTGCTTAATTACCCTGAATTAAGTTACTTATT
78449 ACTAATTCAC
Statistics
Matches: 192, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
105 23 0.12
108 167 0.87
109 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (108 bp):
CTTAATTACCCTGAATTAAGTTATTTATTGCTGATTTACTTAATTACCCTGAATTAAGTTATCTA
CCTACTTGCTTAATTACCCTGAATTAAGTTACTTATTGACTCA
Found at i:78331 original size:143 final size:141
Alignment explanation
Indices: 78134--78441 Score: 386
Period size: 143 Copynumber: 2.2 Consensus size: 141
78124 TTAAGTCGAT
*
78134 CTTAATTACCCTGAATTAAGTTAACTACTGACTCACTTGACTACCCCGAATTAAGTTACTTATTA
1 CTTAATTACCCTGAATTAAGTTAACTACTGACTCACTTAACTACCCCGAATTAAGTTACTTATTA
** *
78199 ACTTGCTTGATTACCCTGAATTAAGTTACTTATTG-ACTCACTTAATTACCCTGAATTAAGTTAT
66 ACTCACTTAATTACCCTGAATTAAGTTACTTATTGAACTCACTTAATTACCCTGAATTAAGTTAT
* * *
78263 TTATTGCTGATTTA
131 CTA---CCGACTTA
* ** * *
78277 CTTAATTACCCTGAATTAAGTTATCTACCT-ACTTGCTTAATTACCCTGAATTAAGTTACTTATT
1 CTTAATTACCCTGAATTAAGTTAACTA-CTGACTCACTTAACTACCCCGAATTAAGTTACTTATT
* * * * *
78341 GACTCACTTAATTACCCTGAATTAAGTTATTTTTTGCTAATTTACTTAATTACCCTGAATTAAGT
65 AACTCACTTAATTACCCTGAATTAAGTTACTTATTG--AACTCACTTAATTACCCTGAATTAAGT
*
78406 TATCTACCGACTTG
128 TATCTACCGACTTA
78420 CTTAATTACCCTGAATTAAGTT
1 CTTAATTACCCTGAATTAAGTT
78442 GCTTATTACT
Statistics
Matches: 143, Mismatches: 18, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
143 112 0.78
144 2 0.01
146 29 0.20
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (141 bp):
CTTAATTACCCTGAATTAAGTTAACTACTGACTCACTTAACTACCCCGAATTAAGTTACTTATTA
ACTCACTTAATTACCCTGAATTAAGTTACTTATTGAACTCACTTAATTACCCTGAATTAAGTTAT
CTACCGACTTA
Found at i:79161 original size:22 final size:23
Alignment explanation
Indices: 79136--79178 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
79126 AAAATTTACC
79136 AAGACTCA-ATCTTT-TTTAAACA
1 AAGA-TCATATCTTTATTTAAACA
*
79158 AAGATCATATTTTTATTTAAA
1 AAGATCATATCTTTATTTAAA
79179 AACAAAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 3 0.17
22 9 0.50
23 6 0.33
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.42
Consensus pattern (23 bp):
AAGATCATATCTTTATTTAAACA
Found at i:80310 original size:33 final size:33
Alignment explanation
Indices: 80240--80326 Score: 115
Period size: 33 Copynumber: 2.6 Consensus size: 33
80230 AAGGATCGTG
**
80240 TGGCCGGTTGTGGCCGGGCATGGTCGAGTCATG
1 TGGCCGGTTGTGGCCGGGCATGGTCGAGTCACA
*
80273 TGGCCGGTTGTGGCCGGGCATGGTC-ATGTCGCA
1 TGGCCGGTTGTGGCCGGGCATGGTCGA-GTCACA
80306 TGGCCGG-TGATGGCCGGGCAT
1 TGGCCGGTTG-TGGCCGGGCAT
80327 CTCCAAGTCG
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
32 3 0.06
33 46 0.94
ACGTcount: A:0.09, C:0.23, G:0.45, T:0.23
Consensus pattern (33 bp):
TGGCCGGTTGTGGCCGGGCATGGTCGAGTCACA
Found at i:80337 original size:33 final size:32
Alignment explanation
Indices: 80240--80348 Score: 103
Period size: 33 Copynumber: 3.3 Consensus size: 32
80230 AAGGATCGTG
* * ***
80240 TGGCCGGTTGTGGCCGGGCATGGTCGAGTCATG
1 TGGCCGG-TGTGGCCGGGCATGCTCAAGTCGCA
* *
80273 TGGCCGGTTGTGGCCGGGCATGGTCATGTCGCA
1 TGGCCGG-TGTGGCCGGGCATGCTCAAGTCGCA
*
80306 TGGCCGGTGATGGCCGGGCAT-CTCCAAGTCGCG
1 TGGCCGGTG-TGGCCGGGCATGCT-CAAGTCGCA
80339 TGGCCGGTGT
1 TGGCCGGTGT
80349 TGCGCAGCTT
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
32 4 0.06
33 62 0.94
ACGTcount: A:0.09, C:0.25, G:0.43, T:0.23
Consensus pattern (32 bp):
TGGCCGGTGTGGCCGGGCATGCTCAAGTCGCA
Done.