Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006696.1 Hibiscus syriacus cultivar Beakdansim tig00016658_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: 205036
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:1021 original size:16 final size:17
Alignment explanation
Indices: 1000--1034 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
990 CTGGCGCGTG
1000 GAATT-CACGCGCCAGC
1 GAATTCCACGCGCCAGC
1016 GAATTCCACGCGCCAGC
1 GAATTCCACGCGCCAGC
1033 GA
1 GA
1035 GACATCCGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (17 bp):
GAATTCCACGCGCCAGC
Found at i:6323 original size:2 final size:2
Alignment explanation
Indices: 6316--6344 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6306 TGTACATCCC
6316 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6345 GGGAGTTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8094 original size:14 final size:14
Alignment explanation
Indices: 8066--8110 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
8056 ACTAAATAAA
*
8066 TAAAATAGT-AAAT
1 TAAAATAATGAAAT
8079 TAAAATAATGAAAT
1 TAAAATAATGAAAT
* *
8093 TAAATTATTGAAAT
1 TAAAATAATGAAAT
8107 TAAA
1 TAAA
8111 TAAATAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 8 0.29
14 20 0.71
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (14 bp):
TAAAATAATGAAAT
Found at i:39627 original size:32 final size:32
Alignment explanation
Indices: 39591--39684 Score: 179
Period size: 32 Copynumber: 2.9 Consensus size: 32
39581 TTAGTCTGAC
*
39591 CACACTAATGGAAAAATAGGGATAAGTAAAAT
1 CACACTAATGGAAAAGTAGGGATAAGTAAAAT
39623 CACACTAATGGAAAAGTAGGGATAAGTAAAAT
1 CACACTAATGGAAAAGTAGGGATAAGTAAAAT
39655 CACACTAATGGAAAAGTAGGGATAAGTAAA
1 CACACTAATGGAAAAGTAGGGATAAGTAAA
39685 CATCTTCAGT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.51, C:0.10, G:0.21, T:0.18
Consensus pattern (32 bp):
CACACTAATGGAAAAGTAGGGATAAGTAAAAT
Found at i:41604 original size:3 final size:3
Alignment explanation
Indices: 41596--41637 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
41586 AGCGACACTT
41596 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41638 CGTGACAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:42368 original size:54 final size:53
Alignment explanation
Indices: 42304--42408 Score: 165
Period size: 54 Copynumber: 2.0 Consensus size: 53
42294 CATTTCACCG
* *
42304 TTATTTTCTCTTGACAATTATGCATTGTTTAATATTGCTTTCAAATCACCAAGT
1 TTATTCTCTCTTGACAATTAAGCATTGTTTAATA-TGCTTTCAAATCACCAAGT
**
42358 TTATTCTCTCTTGACAATTAAGCATTGTTTTGTATGCTTTCAAATCACCAA
1 TTATTCTCTCTTGACAATTAAGCATTGTTTAATATGCTTTCAAATCACCAA
42409 TTTGATCATG
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 17 0.36
54 30 0.64
ACGTcount: A:0.28, C:0.18, G:0.10, T:0.45
Consensus pattern (53 bp):
TTATTCTCTCTTGACAATTAAGCATTGTTTAATATGCTTTCAAATCACCAAGT
Found at i:44908 original size:27 final size:27
Alignment explanation
Indices: 44877--44946 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
44867 ATTGAATCTG
*
44877 AAAGATTGACTCCTCTACAGGAATAGA-
1 AAAGATTGACTTCTCTACAGGAATA-AC
* **
44904 AAAGATTGACTTCTTTTTAGGAATAAC
1 AAAGATTGACTTCTCTACAGGAATAAC
44931 AAAGATTGACTTCTCT
1 AAAGATTGACTTCTCT
44947 TCACGAGGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 1 0.03
27 36 0.97
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (27 bp):
AAAGATTGACTTCTCTACAGGAATAAC
Found at i:45030 original size:67 final size:66
Alignment explanation
Indices: 44922--45414 Score: 429
Period size: 67 Copynumber: 7.9 Consensus size: 66
44912 ACTTCTTTTT
*
44922 AGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAATGATTGATTCCTCTTCACGAGGGAG
1 AGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGATTCCTCTTCACGA-GGAG
44987 TC
65 TC
* * * *
44989 AGGAATAACAAATG-TTGACTTATCTTCACGAGGAAGTCAATGATTAACTCCTCTT---------
1 AGGAATAACAAA-GATTGACTTCTCTTCACGAGGAAGTCAAGGATTGATTCCTCTTCACGAGGAG
45044 T-
65 TC
* * *
45045 AGGAATAACAAAGATTGACTTCTCTTAATGAGGAAGTCAAGGATTGGTTCCTCTTCACGAGGGAG
1 AGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGATTCCTCTTCACGA-GGAG
45110 TC
65 TC
* * * * * *
45112 TGGAATAACAAAGATTGGCTTCTATTCACGAGGAAGTCAAGGATT-A----AC-TC-C---TATT
1 AGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGATTCCTCTTCACGAGGAGT
45167 C
66 C
* * *
45168 AGGAATAACAAAGATTGATTTCTCTTCACGAGGAAGCCAAGGATTG-GTCCATCTTCACGATGGA
1 AGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGATTCC-TCTTCACGA-GGA
45232 GTC
64 GTC
* * * * *
45235 TGGAATAACAAAGATTGACTTCTCTTCATGAGGAAGTCAATGATTGA---CTCAT--C-----TT
1 AGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGATTCCTCTTCACGAGGAGT
45290 C
66 C
* * *
45291 AGGAATAACAAAGATTGACTTCTCTTCAAGAGGAAGTCAACGATTGGTTCCTCTTCACGAGGGAG
1 AGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGATTCCTCTTCACGA-GGAG
45356 TC
65 TC
* * * * * *
45358 CGGAATAACAAAGATTGACTTCTATTCAAGAAGAAGTCAAGGATTGACTCCTATTCA
1 AGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGATTCCTCTTCA
45415 ATAAGAAGTC
Statistics
Matches: 342, Mismatches: 47, Indels: 74
0.74 0.10 0.16
Matches are distributed among these distances:
55 1 0.00
56 134 0.39
57 1 0.00
59 4 0.01
60 1 0.00
61 4 0.01
62 4 0.01
63 1 0.00
64 3 0.01
65 1 0.00
66 1 0.00
67 186 0.54
68 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (66 bp):
AGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGATTCCTCTTCACGAGGAGT
C
Found at i:45078 original size:56 final size:56
Alignment explanation
Indices: 44989--45335 Score: 257
Period size: 56 Copynumber: 5.8 Consensus size: 56
44979 CGAGGGAGTC
* *
44989 AGGAATAACAAATG-TTGACTTATCTTCACGAGGAAGTCAATGATTAACTCCTCTTT
1 AGGAATAACAAA-GATTGACTTCTCTTCACGAGGAAGTCAAGGATTAACTCCTCTTT
* * ***
45045 AGGAATAACAAAGATTGACTTCTCTTAATGAGGAAGTCAAGGATTGGTTCCTCTTCACGAGGGAG
1 AGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTAACTCCTCTT----------
45110 T
56 T
* * * * *
45111 CTGGAATAACAAAGATTGGCTTCTATTCACGAGGAAGTCAAGGATTAACTCCTATTC
1 -AGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTAACTCCTCTTT
* * **
45168 AGGAATAACAAAGATTGATTTCTCTTCACGAGGAAGCCAAGGATT-GGTCCATCTTCACGAT
1 AGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTAACTCC-TCTT-----T
* * * * *
45229 GGAGTCTGGAATAACAAAGATTGACTTCTCTTCATGAGGAAGTCAATGATTGACTCATCTTC
1 --A----GGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTAACTCCTCTTT
* *
45291 AGGAATAACAAAGATTGACTTCTCTTCAAGAGGAAGTCAACGATT
1 AGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATT
45336 GGTTCCTCTT
Statistics
Matches: 230, Mismatches: 36, Indels: 50
0.73 0.11 0.16
Matches are distributed among these distances:
55 4 0.02
56 131 0.57
60 1 0.00
63 1 0.00
66 1 0.00
67 90 0.39
68 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (56 bp):
AGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTAACTCCTCTTT
Found at i:45078 original size:123 final size:123
Alignment explanation
Indices: 44922--45414 Score: 704
Period size: 123 Copynumber: 4.0 Consensus size: 123
44912 ACTTCTTTTT
* * *
44922 AGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAATGATTGATTCCTCTTCACGAGGGAG
1 AGGAATAACAAAGATTGACTTCTCTTAACGAGGAAGTCAAGGATTGGTTCCTCTTCACGAGGGAG
* * * * *
44987 TCAGGAATAACAAATG-TTGACTTATCTTCACGAGGAAGTCAATGATTAACTCCTCTTT
66 TCTGGAATAACAAA-GATTGACTTCTATTCACGAGGAAGTCAAGGATTAACTCCTCTTC
*
45045 AGGAATAACAAAGATTGACTTCTCTTAATGAGGAAGTCAAGGATTGGTTCCTCTTCACGAGGGAG
1 AGGAATAACAAAGATTGACTTCTCTTAACGAGGAAGTCAAGGATTGGTTCCTCTTCACGAGGGAG
* *
45110 TCTGGAATAACAAAGATTGGCTTCTATTCACGAGGAAGTCAAGGATTAACTCCTATTC
66 TCTGGAATAACAAAGATTGACTTCTATTCACGAGGAAGTCAAGGATTAACTCCTCTTC
* * * *
45168 AGGAATAACAAAGATTGATTTCTCTTCACGAGGAAGCCAAGGATTGG-TCCATCTTCACGATGGA
1 AGGAATAACAAAGATTGACTTCTCTTAACGAGGAAGTCAAGGATTGGTTCC-TCTTCACGAGGGA
* * * * *
45232 GTCTGGAATAACAAAGATTGACTTCTCTTCATGAGGAAGTCAATGATTGACTCATCTTC
65 GTCTGGAATAACAAAGATTGACTTCTATTCACGAGGAAGTCAAGGATTAACTCCTCTTC
*
45291 AGGAATAACAAAGATTGACTTCTCTTCAA-GAGGAAGTCAACGATTGGTTCCTCTTCACGAGGGA
1 AGGAATAACAAAGATTGACTTCTCTT-AACGAGGAAGTCAAGGATTGGTTCCTCTTCACGAGGGA
* * * * *
45355 GTCCGGAATAACAAAGATTGACTTCTATTCAAGAAGAAGTCAAGGATTGACTCCTATTC
65 GTCTGGAATAACAAAGATTGACTTCTATTCACGAGGAAGTCAAGGATTAACTCCTCTTC
45414 A
1 A
45415 ATAAGAAGTC
Statistics
Matches: 331, Mismatches: 35, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
122 4 0.01
123 323 0.98
124 4 0.01
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (123 bp):
AGGAATAACAAAGATTGACTTCTCTTAACGAGGAAGTCAAGGATTGGTTCCTCTTCACGAGGGAG
TCTGGAATAACAAAGATTGACTTCTATTCACGAGGAAGTCAAGGATTAACTCCTCTTC
Found at i:45307 original size:27 final size:27
Alignment explanation
Indices: 45236--45318 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
45226 GATGGAGTCT
45236 GGAATAACAAAGATTGACTTCTCTTCA
1 GGAATAACAAAGATTGACTTCTCTTCA
* ** *
45263 TGAGGAAGTCAATGATTGAC-TCATCTTCA
1 GGAATAA--CAAAGATTGACTTC-TCTTCA
45292 GGAATAACAAAGATTGACTTCTCTTCA
1 GGAATAACAAAGATTGACTTCTCTTCA
45319 AGAGGAAGTC
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
27 20 0.45
28 4 0.09
29 20 0.45
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (27 bp):
GGAATAACAAAGATTGACTTCTCTTCA
Found at i:45356 original size:246 final size:246
Alignment explanation
Indices: 44922--45414 Score: 785
Period size: 246 Copynumber: 2.0 Consensus size: 246
44912 ACTTCTTTTT
* * *
44922 AGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAATGATTGATTCCTCTTCACGAGGGAG
1 AGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGCCAAGGATTGAGTCCTCTTCACGAGGGAG
* *
44987 TCAGGAATAACAAATGTTGACTTATCTTCACGAGGAAGTCAATGATTAACTCCTCTTTAGGAATA
66 TCAGGAATAACAAATGTTGACTTATCTTCACGAGGAAGTCAATGATTAACTCATCTTCAGGAATA
* *
45052 ACAAAGATTGACTTCTCTTAATGAGGAAGTCAAGGATTGGTTCCTCTTCACGAGGGAGTCTGGAA
131 ACAAAGATTGACTTCTCTTAATGAGGAAGTCAACGATTGGTTCCTCTTCACGAGGGAGTCCGGAA
* * *
45117 TAACAAAGATTGGCTTCTATTCACGAGGAAGTCAAGGATTAACTCCTATTC
196 TAACAAAGATTGACTTCTATTCAAGAAGAAGTCAAGGATTAACTCCTATTC
* *
45168 AGGAATAACAAAGATTGATTTCTCTTCACGAGGAAGCCAAGGATTG-GTCCATCTTCACGATGGA
1 AGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGCCAAGGATTGAGTCC-TCTTCACGAGGGA
* * * *
45232 GTCTGGAATAACAAA-GATTGACTTCTCTTCATGAGGAAGTCAATGATTGACTCATCTTCAGGAA
65 GTCAGGAATAACAAATG-TTGACTTATCTTCACGAGGAAGTCAATGATTAACTCATCTTCAGGAA
45296 TAACAAAGATTGACTTCTCTTCAA-GAGGAAGTCAACGATTGGTTCCTCTTCACGAGGGAGTCCG
129 TAACAAAGATTGACTTCTCTT-AATGAGGAAGTCAACGATTGGTTCCTCTTCACGAGGGAGTCCG
*
45360 GAATAACAAAGATTGACTTCTATTCAAGAAGAAGTCAAGGATTGACTCCTATTC
193 GAATAACAAAGATTGACTTCTATTCAAGAAGAAGTCAAGGATTAACTCCTATTC
45414 A
1 A
45415 ATAAGAAGTC
Statistics
Matches: 227, Mismatches: 17, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
245 4 0.02
246 221 0.97
247 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (246 bp):
AGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGCCAAGGATTGAGTCCTCTTCACGAGGGAG
TCAGGAATAACAAATGTTGACTTATCTTCACGAGGAAGTCAATGATTAACTCATCTTCAGGAATA
ACAAAGATTGACTTCTCTTAATGAGGAAGTCAACGATTGGTTCCTCTTCACGAGGGAGTCCGGAA
TAACAAAGATTGACTTCTATTCAAGAAGAAGTCAAGGATTAACTCCTATTC
Found at i:45459 original size:123 final size:122
Alignment explanation
Indices: 44922--45480 Score: 604
Period size: 123 Copynumber: 4.5 Consensus size: 122
44912 ACTTCTTTTT
* * * * *
44922 AGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAATGATTGATTCCTCTTCACGAGGGAG
1 AGGAATAACAAAGATTGACTCCTCTTCAGGAAGAAG-CAAGGATTGGTTCCTCTTCACGAGGGAG
* * * * * *
44987 TCAGGAATAACAAATG-TTGACTTATCTTCACGAGGAAGTCAATGATTAACTCCTCTTT
65 TCTGGAATAACAAA-GATTGACTTCTATTCACGAGGAAGTCAAGGATTAACTCCTATTC
* * * *
45045 AGGAATAACAAAGATTGACTTCTCTTAATGAGGAAGTCAAGGATTGGTTCCTCTTCACGAGGGAG
1 AGGAATAACAAAGATTGACTCCTCTTCAGGAAGAAG-CAAGGATTGGTTCCTCTTCACGAGGGAG
*
45110 TCTGGAATAACAAAGATTGGCTTCTATTCACGAGGAAGTCAAGGATTAACTCCTATTC
65 TCTGGAATAACAAAGATTGACTTCTATTCACGAGGAAGTCAAGGATTAACTCCTATTC
* * * * *
45168 AGGAATAACAAAGATTGATTTCTCTTCACGAGGAAGCCAAGGATTGG-TCCATCTTCACGATGGA
1 AGGAATAACAAAGATTGACTCCTCTTCAGGAAGAAG-CAAGGATTGGTTCC-TCTTCACGAGGGA
* * * * * *
45232 GTCTGGAATAACAAAGATTGACTTCTCTTCATGAGGAAGTCAATGATTGACTCATCTTC
64 GTCTGGAATAACAAAGATTGACTTCTATTCACGAGGAAGTCAAGGATTAACTCCTATTC
* * * *
45291 AGGAATAACAAAGATTGACTTCTCTTCAAGAGGAAGTCAACGATTGGTTCCTCTTCACGAGGGAG
1 AGGAATAACAAAGATTGACTCCTCTTCAGGAAGAAG-CAAGGATTGGTTCCTCTTCACGAGGGAG
* * * *
45356 TCCGGAATAACAAAGATTGACTTCTATTCAAGAAGAAGTCAAGGATTGACTCCTATTC
65 TCTGGAATAACAAAGATTGACTTCTATTCACGAGGAAGTCAAGGATTAACTCCTATTC
** * * * * * * * *
45414 AATAAGAAGTCAATGATTGACTCCTTTTTAGGAATAA-CAAAGATTGACTT-CTCTTCACGAGGA
1 AGGAATAA--CAAAGATTGACTCCTCTTCAGGAAGAAGCAAGGATTG-GTTCCTCTTCACGAGGG
45477 AGTC
63 AGTC
45481 AAGGATTGGT
Statistics
Matches: 382, Mismatches: 48, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
122 4 0.01
123 353 0.92
124 5 0.01
125 20 0.05
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (122 bp):
AGGAATAACAAAGATTGACTCCTCTTCAGGAAGAAGCAAGGATTGGTTCCTCTTCACGAGGGAGT
CTGGAATAACAAAGATTGACTTCTATTCACGAGGAAGTCAAGGATTAACTCCTATTC
Found at i:45471 original size:246 final size:244
Alignment explanation
Indices: 44928--45481 Score: 718
Period size: 246 Copynumber: 2.2 Consensus size: 244
44918 TTTTAGGAAT
* * * *
44928 AACAAAGATTGACTTCTCTTCACGAGGAAGTCAATGATTGATTCCTCTTCACGAGGGAGTCAGGA
1 AACAAAGATTGACTCCTCTTCACGAAGAA-CCAAAGATTGATT-CTCTTCACGAGGGAGTCAGGA
* *
44993 ATAACAAATGTTGACTTATCTTCACGAGGAAGTCAATGATTAACTCCTCTTTAGGAATAACAAAG
64 ATAACAAATGTTGACTTATCTTCACGAGGAAGTCAATGATTAACTCATCTTCAGGAATAACAAAG
* *
45058 ATTGACTTCTCTTAATGAGGAAGTCAAGGATTGGTTCCTCTTCACGAGGGAGTCTGGAATAACAA
129 ATTGACTTCTCTTAATGAGGAAGTCAACGATTGGTTCCTCTTCACGAGGGAGTCCGGAATAACAA
* * * * *
45123 AGATTGGCTTCTATTCACGAGGAAGTCAAGGATTAACTCCTATTCAGGAAT
194 AGATTGACTTCTATTCAAGAAGAAGTCAAGGATTAACTCCTATTCAAGAAG
* * * * * * * *
45174 AACAAAGATTGATTTCTCTTCACGAGGAAGCCAAGGATTGGTCCATCTTCACGATGGAGTCTGGA
1 AACAAAGATTGACTCCTCTTCACGAAGAA-CCAAAGATTGATTC-TCTTCACGAGGGAGTCAGGA
* * *
45239 ATAACAAA-GATTGACTTCTCTTCATGAGGAAGTCAATGATTGACTCATCTTCAGGAATAACAAA
64 ATAACAAATG-TTGACTTATCTTCACGAGGAAGTCAATGATTAACTCATCTTCAGGAATAACAAA
45303 GATTGACTTCTCTTCAA-GAGGAAGTCAACGATTGGTTCCTCTTCACGAGGGAGTCCGGAATAAC
128 GATTGACTTCTCTT-AATGAGGAAGTCAACGATTGGTTCCTCTTCACGAGGGAGTCCGGAATAAC
* *
45367 AAAGATTGACTTCTATTCAAGAAGAAGTCAAGGATTGACTCCTATTCAATAAG
192 AAAGATTGACTTCTATTCAAGAAGAAGTCAAGGATTAACTCCTATTCAAGAAG
* * * * * *
45420 AAGTCAATGATTGACTCCTTTTTAGGAATAA-CAAAGATTGACTTCTCTTCACGAGGAAGTCA
1 AA--CAAAGATTGACTCCTCTTCACGAAGAACCAAAGATTGA-TTCTCTTCACGAGGGAGTCA
45482 AGGATTGGTT
Statistics
Matches: 267, Mismatches: 35, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
245 2 0.01
246 242 0.91
247 4 0.01
248 19 0.07
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (244 bp):
AACAAAGATTGACTCCTCTTCACGAAGAACCAAAGATTGATTCTCTTCACGAGGGAGTCAGGAAT
AACAAATGTTGACTTATCTTCACGAGGAAGTCAATGATTAACTCATCTTCAGGAATAACAAAGAT
TGACTTCTCTTAATGAGGAAGTCAACGATTGGTTCCTCTTCACGAGGGAGTCCGGAATAACAAAG
ATTGACTTCTATTCAAGAAGAAGTCAAGGATTAACTCCTATTCAAGAAG
Found at i:46602 original size:15 final size:17
Alignment explanation
Indices: 46582--46614 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
46572 TACCTTTATG
46582 TCTCAAAT-AATG-TCT
1 TCTCAAATCAATGATCT
46597 TCTCAAATCAATGATCT
1 TCTCAAATCAATGATCT
46614 T
1 T
46615 GCATTCCCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 4 0.25
17 4 0.25
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.39
Consensus pattern (17 bp):
TCTCAAATCAATGATCT
Found at i:50538 original size:18 final size:18
Alignment explanation
Indices: 50515--50549 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
50505 GCACTTGAAA
50515 TTTGTCCCAAATGACCAT
1 TTTGTCCCAAATGACCAT
*
50533 TTTGTCCCGAATGACCA
1 TTTGTCCCAAATGACCA
50550 CTATCCATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (18 bp):
TTTGTCCCAAATGACCAT
Found at i:50588 original size:31 final size:31
Alignment explanation
Indices: 50550--50643 Score: 102
Period size: 31 Copynumber: 3.0 Consensus size: 31
50540 CGAATGACCA
50550 CTATCCATAAGTCCCGAAGGACATAAGTAAC
1 CTATCCATAAGTCCCGAAGGACATAAGTAAC
* ** *
50581 CTATCCATATGTCCTAAAGGACAT-AGCTAAA
1 CTATCCATAAGTCCCGAAGGACATAAG-TAAC
* *
50612 CTGTCCATATA-TCCCGAAGGACATAGGTAAC
1 CTATCCATA-AGTCCCGAAGGACATAAGTAAC
50643 C
1 C
50644 CTCAACTCTT
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
30 2 0.04
31 47 0.94
32 1 0.02
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (31 bp):
CTATCCATAAGTCCCGAAGGACATAAGTAAC
Found at i:52846 original size:21 final size:19
Alignment explanation
Indices: 52804--52846 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
52794 AAAATAAAAA
*
52804 CAAAATAAAATCTGGAATT
1 CAAAATAAAATCTGGAAAT
*
52823 CAAATTAAAATACATGGAAAT
1 CAAAATAAAAT-C-TGGAAAT
52844 CAA
1 CAA
52847 TTACAATTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 10 0.50
20 1 0.05
21 9 0.45
ACGTcount: A:0.56, C:0.12, G:0.09, T:0.23
Consensus pattern (19 bp):
CAAAATAAAATCTGGAAAT
Found at i:59985 original size:5 final size:5
Alignment explanation
Indices: 59975--60000 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
59965 GCAGAGGCTG
59975 CTTCT CTTCT CTTCT CTTCT CTTCT C
1 CTTCT CTTCT CTTCT CTTCT CTTCT C
60001 CGATCAAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (5 bp):
CTTCT
Found at i:61829 original size:167 final size:167
Alignment explanation
Indices: 61529--61845 Score: 494
Period size: 167 Copynumber: 1.9 Consensus size: 167
61519 CTGCAACCAG
* * * *
61529 AACAAAAGATATGGGTTTTGGGTTTAATGGCATTGTCTCGTAGTAGTTCAATTCCAGTGCAGTAA
1 AACAAAAGATATGGGCTTTAGGTTTAATGGCATTGTCTCATAGTAGCTCAATTCCAGTGCAGTAA
* *
61594 TAAGAACGATAACTAAATAATTTATATCAGCCTTCTAGATAGATGTTGCTTACAAATGCCCTAAG
66 TAAGAACGATAACTAAATAATTTATATCAGCCTTCTAGATAGATATTGCTAACAAATGCCCTAAG
*
61659 GTGCTAGTTCGTTCGAGTAATTTTCTGGTATTGCTAT
131 GTGCTAGGTCGTTCGAGTAATTTTCTGGTATTGCTAT
61696 AACAAAAGATATGGGCTTTAGGTTTAATGGCATTGTCTCATAGTAGCTCAATTCCAGTGCAGTAA
1 AACAAAAGATATGGGCTTTAGGTTTAATGGCATTGTCTCATAGTAGCTCAATTCCAGTGCAGTAA
* * * * *
61761 TCAGAACGATAACT-AGTAATTTATA-CATGGCTTCTAGTTAGGTATTGCTAACAAATGCCCTAA
66 TAAGAACGATAACTAAATAATTTATATCA-GCCTTCTAGATAGATATTGCTAACAAATGCCCT-A
61824 AGGTGCTAGGTCGTTCGAGTAA
129 AGGTGCTAGGTCGTTCGAGTAA
61846 CTTACCAGTC
Statistics
Matches: 136, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
165 2 0.01
166 38 0.28
167 96 0.71
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (167 bp):
AACAAAAGATATGGGCTTTAGGTTTAATGGCATTGTCTCATAGTAGCTCAATTCCAGTGCAGTAA
TAAGAACGATAACTAAATAATTTATATCAGCCTTCTAGATAGATATTGCTAACAAATGCCCTAAG
GTGCTAGGTCGTTCGAGTAATTTTCTGGTATTGCTAT
Found at i:64046 original size:36 final size:36
Alignment explanation
Indices: 64006--64346 Score: 305
Period size: 36 Copynumber: 9.8 Consensus size: 36
63996 CAGAAGCCAG
* *
64006 TTCATGTTGAGGCTCATCCTGAGGTTCAGTTGCTAA
1 TTCATGTTGAGGCTCATCCTGAGGTTCAGTAGCTGA
* *
64042 TTCATGTTGAGGCACAAT-CTGAGGTTCAGTAGCTAA
1 TTCATGTTGAGGCTC-ATCCTGAGGTTCAGTAGCTGA
** * *
64078 TTCATGTTGAATCTTATCCTTAGGTTCAGTAGCTGA
1 TTCATGTTGAGGCTCATCCTGAGGTTCAGTAGCTGA
* * *** *
64114 TTCGTATTGAGGCTCAGGTTGAGGCTCAGTAGCTGA
1 TTCATGTTGAGGCTCATCCTGAGGTTCAGTAGCTGA
* *
64150 TTCATGTTGAGGCTCAGCCTGCGGTTCAGTAGCTGA
1 TTCATGTTGAGGCTCATCCTGAGGTTCAGTAGCTGA
*
64186 TTCACGTTGAGG--C-T-C--A-G-T-A--A-CTGA
1 TTCATGTTGAGGCTCATCCTGAGGTTCAGTAGCTGA
* *
64210 TTCATGTTGAGGCTCAGCCTGAGGTTCAGTAGCCGA
1 TTCATGTTGAGGCTCATCCTGAGGTTCAGTAGCTGA
* * *
64246 TTCATGTTGAGGCTCAGCCTGAGGTTCACTAGCCGA
1 TTCATGTTGAGGCTCATCCTGAGGTTCAGTAGCTGA
* * *
64282 TTCATGTTGTA-GCTCAGCCTGAGGTTCACTAGCCGA
1 TTCATGTTG-AGGCTCATCCTGAGGTTCAGTAGCTGA
* * * *
64318 TTCATGTTGTGGCTTAGCTTGAGGTTCAG
1 TTCATGTTGAGGCTCATCCTGAGGTTCAG
64347 GATCAAACTC
Statistics
Matches: 254, Mismatches: 35, Indels: 32
0.79 0.11 0.10
Matches are distributed among these distances:
24 15 0.06
25 1 0.00
26 1 0.00
27 1 0.00
28 2 0.01
29 1 0.00
30 1 0.00
31 1 0.00
32 2 0.01
33 1 0.00
34 1 0.00
35 3 0.01
36 221 0.87
37 3 0.01
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (36 bp):
TTCATGTTGAGGCTCATCCTGAGGTTCAGTAGCTGA
Found at i:64209 original size:24 final size:24
Alignment explanation
Indices: 64175--64226 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
64165 AGCCTGCGGT
*
64175 TCAGTAGCTGATTCACGTTGAGGC
1 TCAGTAACTGATTCACGTTGAGGC
*
64199 TCAGTAACTGATTCATGTTGAGGC
1 TCAGTAACTGATTCACGTTGAGGC
64223 TCAG
1 TCAG
64227 CCTGAGGTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (24 bp):
TCAGTAACTGATTCACGTTGAGGC
Found at i:64224 original size:60 final size:60
Alignment explanation
Indices: 64131--64262 Score: 228
Period size: 60 Copynumber: 2.2 Consensus size: 60
64121 TGAGGCTCAG
* * *
64131 GTTGAGGCTCAGTAGCTGATTCATGTTGAGGCTCAGCCTGCGGTTCAGTAGCTGATTCAC
1 GTTGAGGCTCAGTAACTGATTCATGTTGAGGCTCAGCCTGAGGTTCAGTAGCCGATTCAC
*
64191 GTTGAGGCTCAGTAACTGATTCATGTTGAGGCTCAGCCTGAGGTTCAGTAGCCGATTCAT
1 GTTGAGGCTCAGTAACTGATTCATGTTGAGGCTCAGCCTGAGGTTCAGTAGCCGATTCAC
64251 GTTGAGGCTCAG
1 GTTGAGGCTCAG
64263 CCTGAGGTTC
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 68 1.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (60 bp):
GTTGAGGCTCAGTAACTGATTCATGTTGAGGCTCAGCCTGAGGTTCAGTAGCCGATTCAC
Found at i:64233 original size:96 final size:96
Alignment explanation
Indices: 64103--64298 Score: 277
Period size: 96 Copynumber: 2.0 Consensus size: 96
64093 ATCCTTAGGT
* * ** *
64103 TCAGTAGCTGATTCGTATTGAGGCTCAGGTTGAGGCTCAGTAGCTGATTCATGTTGAGGCTCAGC
1 TCAGTAACTGATTCATATTGAGGCTCAGCCTGAGGCTCAGTAGCCGATTCATGTTGAGGCTCAGC
* * *
64168 CTGCGGTTCAGTAGCTGATTCACGTTG-AGGC
66 CTGAGGTTCACTAGCCGATTCACGTTGTA-GC
* *
64199 TCAGTAACTGATTCATGTTGAGGCTCAGCCTGAGGTTCAGTAGCCGATTCATGTTGAGGCTCAGC
1 TCAGTAACTGATTCATATTGAGGCTCAGCCTGAGGCTCAGTAGCCGATTCATGTTGAGGCTCAGC
*
64264 CTGAGGTTCACTAGCCGATTCATGTTGTAGC
66 CTGAGGTTCACTAGCCGATTCACGTTGTAGC
64295 TCAG
1 TCAG
64299 CCTGAGGTTC
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
96 87 0.99
97 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (96 bp):
TCAGTAACTGATTCATATTGAGGCTCAGCCTGAGGCTCAGTAGCCGATTCATGTTGAGGCTCAGC
CTGAGGTTCACTAGCCGATTCACGTTGTAGC
Found at i:64262 original size:132 final size:132
Alignment explanation
Indices: 64061--64331 Score: 337
Period size: 132 Copynumber: 2.1 Consensus size: 132
64051 AGGCACAATC
* * * * * * * *
64061 TGAGGTTCAGTAGCTAATTCATGTTGAATCTTATCCTTAGGTTCAGTAGCTGATTCGTATTGAGG
1 TGAGGCTCAGTAACTAATTCATGTTGAAGCTCAGCCTGAGGTTCAGTAGCCGATTCATATTGAGG
** * * * * *
64126 CTCAGGTTGAGGCTCAGTAGCTGATTCATGTTG-AGGCTCAGCCTGCGGTTCAGTAGCTGATTCA
66 CTCAGCCTGAGGCTCACTAGCCGATTCATGTTGTA-GCTCAGCCTGAGGTTCACTAGCCGATTCA
64190 CGT
130 CGT
* * *
64193 TGAGGCTCAGTAACTGATTCATGTTGAGGCTCAGCCTGAGGTTCAGTAGCCGATTCATGTTGAGG
1 TGAGGCTCAGTAACTAATTCATGTTGAAGCTCAGCCTGAGGTTCAGTAGCCGATTCATATTGAGG
* *
64258 CTCAGCCTGAGGTTCACTAGCCGATTCATGTTGTAGCTCAGCCTGAGGTTCACTAGCCGATTCAT
66 CTCAGCCTGAGGCTCACTAGCCGATTCATGTTGTAGCTCAGCCTGAGGTTCACTAGCCGATTCAC
64323 GT
131 GT
*
64325 TGTGGCT
1 TGAGGCT
64332 TAGCTTGAGG
Statistics
Matches: 117, Mismatches: 21, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
132 116 0.99
133 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (132 bp):
TGAGGCTCAGTAACTAATTCATGTTGAAGCTCAGCCTGAGGTTCAGTAGCCGATTCATATTGAGG
CTCAGCCTGAGGCTCACTAGCCGATTCATGTTGTAGCTCAGCCTGAGGTTCACTAGCCGATTCAC
GT
Found at i:71544 original size:67 final size:67
Alignment explanation
Indices: 71426--71557 Score: 221
Period size: 67 Copynumber: 2.0 Consensus size: 67
71416 TTGTTTGACT
71426 AGACCTGGAGCTTAAGATAAGAAATTTCATGCAAAATATAAAACTAGTGAAAGACGGAAAGAGTC
1 AGACCTGGAGCTTAAGATAAGAAATTTCATGCAAAATATAAAACTAGTGAAAGACGGAAAGAGTC
71491 TC
66 TC
* * *
71493 AGACTTGGAGCTTAAGA-AACGAAATTTCATGCAAAATATAAAACTATTGAAATACGGAAAGAGT
1 AGACCTGGAGCTTAAGATAA-GAAATTTCATGCAAAATATAAAACTAGTGAAAGACGGAAAGAGT
71557 C
65 C
71558 GAAGAATGTA
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
66 2 0.03
67 59 0.97
ACGTcount: A:0.45, C:0.13, G:0.20, T:0.22
Consensus pattern (67 bp):
AGACCTGGAGCTTAAGATAAGAAATTTCATGCAAAATATAAAACTAGTGAAAGACGGAAAGAGTC
TC
Found at i:72746 original size:20 final size:18
Alignment explanation
Indices: 72699--72746 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 18
72689 CCATTAAGGA
72699 TTATTTTAAGGATTTTTT
1 TTATTTTAAGGATTTTTT
*
72717 TTTTCATTTAAGGATTATTTT
1 TTAT--TTTAAGGATT-TTTT
72738 TTATGTTTA
1 TTAT-TTTA
72747 TGCTCTGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 3 0.12
20 14 0.58
21 7 0.29
ACGTcount: A:0.23, C:0.02, G:0.10, T:0.65
Consensus pattern (18 bp):
TTATTTTAAGGATTTTTT
Found at i:77895 original size:27 final size:25
Alignment explanation
Indices: 77864--77914 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
77854 CTTAAAATTT
* *
77864 TAAAATTTTGCATTCATTCTTCTAACA
1 TAAAATATTACATTCA-TC-TCTAACA
77891 TAAAATATTACATTCATCTCTAAC
1 TAAAATATTACATTCATCTCTAAC
77915 GTTTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 6 0.27
26 2 0.09
27 14 0.64
ACGTcount: A:0.37, C:0.20, G:0.02, T:0.41
Consensus pattern (25 bp):
TAAAATATTACATTCATCTCTAACA
Found at i:87576 original size:16 final size:16
Alignment explanation
Indices: 87557--87590 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
87547 ATAATAATAT
*
87557 AATTTTTAAATAAAAA
1 AATTTATAAATAAAAA
87573 AA-TTATAAATAAAAA
1 AATTTATAAATAAAAA
87588 AAT
1 AAT
87591 ACGTTAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
15 14 0.88
16 2 0.12
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AATTTATAAATAAAAA
Found at i:100984 original size:21 final size:22
Alignment explanation
Indices: 100936--100984 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
100926 AAAAAATTAA
100936 AAATTTAGGTACTAAAACCGAT
1 AAATTTAGGTACTAAAACCGAT
*
100958 -AGTTTAGGTACTAAATA-C-AT
1 AAATTTAGGTACTAAA-ACCGAT
100978 AAATTTA
1 AAATTTA
100985 CCCAAGATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
20 2 0.09
21 20 0.87
22 1 0.04
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (22 bp):
AAATTTAGGTACTAAAACCGAT
Found at i:106921 original size:16 final size:16
Alignment explanation
Indices: 106900--106944 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
106890 TAATAAATAA
106900 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
106916 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
*
106932 ACGATCATAAACG
1 ACGAACATAAACG
106945 TTGGAGACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.53, C:0.22, G:0.13, T:0.11
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:107128 original size:16 final size:16
Alignment explanation
Indices: 107098--107128 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
107088 TGAAACTCGA
*
107098 CTCGAACTCGAAAAAG
1 CTCGAACTCAAAAAAG
107114 CTCGAACTCAAAAAA
1 CTCGAACTCAAAAAA
107129 AAATTAAGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.26, G:0.13, T:0.13
Consensus pattern (16 bp):
CTCGAACTCAAAAAAG
Found at i:107176 original size:11 final size:11
Alignment explanation
Indices: 107160--107245 Score: 61
Period size: 11 Copynumber: 7.5 Consensus size: 11
107150 CTAGAGACTC
107160 AAGCTCGATTG
1 AAGCTCGATTG
107171 AAGCTCGATTCTG
1 AAGCTCGA-T-TG
*
107184 -AGCTCGATTA
1 AAGCTCGATTG
*
107194 AAGGTCGATTCTG
1 AAGCTCGA-T-TG
*
107207 -AGCTCGATTC
1 AAGCTCGATTG
107217 AAGCTCGATTCTG
1 AAGCTCGA-T-TG
*
107230 -AGCTCGATTC
1 AAGCTCGATTG
107240 AAGCTC
1 AAGCTC
107246 AACATTGCCC
Statistics
Matches: 59, Mismatches: 7, Indels: 18
0.70 0.08 0.21
Matches are distributed among these distances:
10 3 0.05
11 29 0.49
12 23 0.39
13 4 0.07
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.29
Consensus pattern (11 bp):
AAGCTCGATTG
Found at i:107189 original size:12 final size:12
Alignment explanation
Indices: 107172--107239 Score: 86
Period size: 12 Copynumber: 5.8 Consensus size: 12
107162 GCTCGATTGA
107172 AGCTCGATTCTG
1 AGCTCGATTCTG
**
107184 AGCTCGATT-AA
1 AGCTCGATTCTG
*
107195 AGGTCGATTCTG
1 AGCTCGATTCTG
*
107207 AGCTCGATTC-A
1 AGCTCGATTCTG
107218 AGCTCGATTCTG
1 AGCTCGATTCTG
107230 AGCTCGATTC
1 AGCTCGATTC
107240 AAGCTCAACA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
11 18 0.39
12 28 0.61
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.31
Consensus pattern (12 bp):
AGCTCGATTCTG
Found at i:107191 original size:23 final size:23
Alignment explanation
Indices: 107161--107245 Score: 143
Period size: 23 Copynumber: 3.7 Consensus size: 23
107151 TAGAGACTCA
*
107161 AGCTCGATTGAAGCTCGATTCTG
1 AGCTCGATTCAAGCTCGATTCTG
* *
107184 AGCTCGATTAAAGGTCGATTCTG
1 AGCTCGATTCAAGCTCGATTCTG
107207 AGCTCGATTCAAGCTCGATTCTG
1 AGCTCGATTCAAGCTCGATTCTG
107230 AGCTCGATTCAAGCTC
1 AGCTCGATTCAAGCTC
107246 AACATTGCCC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (23 bp):
AGCTCGATTCAAGCTCGATTCTG
Found at i:108211 original size:43 final size:40
Alignment explanation
Indices: 108162--108253 Score: 105
Period size: 40 Copynumber: 2.2 Consensus size: 40
108152 TTCACGAACG
* *
108162 TAAATGAACGAACGAGACCTATGTTCATGTCCGTTCATTTAA
1 TAAATGAACG-ACAAAACCT-TGTTCATGTCCGTTCATTTAA
* *
108204 TTAAATGAAC-ACAAAATCTTGTTCATGTTCGTTCATTTAA
1 -TAAATGAACGACAAAACCTTGTTCATGTCCGTTCATTTAA
*
108244 TAAATAAACG
1 TAAATGAACG
108254 CATATAAACG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
39 8 0.19
40 20 0.47
41 6 0.14
43 9 0.21
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (40 bp):
TAAATGAACGACAAAACCTTGTTCATGTCCGTTCATTTAA
Found at i:108531 original size:14 final size:14
Alignment explanation
Indices: 108514--108558 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
108504 AATGAACATA
108514 AACGAACATAACCG
1 AACGAACATAACCG
108528 AACGAACATAACCG
1 AACGAACATAACCG
* *
108542 AACGAATATAATCG
1 AACGAACATAACCG
108556 AAC
1 AAC
108559 ATTCACGAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.51, C:0.24, G:0.13, T:0.11
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:108581 original size:24 final size:24
Alignment explanation
Indices: 108498--108582 Score: 68
Period size: 24 Copynumber: 3.5 Consensus size: 24
108488 GGGTTAAACA
* * *
108498 TAAATGAATGAACATAAACGAACA
1 TAAATGAACGAACATTAACGAACG
**
108522 TAACCGAACGAACA-TAACCGAACG
1 TAAATGAACGAACATTAA-CGAACG
*
108546 -AATAT-AATCGAACATTCACGAACG
1 TAA-ATGAA-CGAACATTAACGAACG
108570 TAAATGAACGAAC
1 TAAATGAACGAAC
108583 GAGACCTATG
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
23 6 0.13
24 35 0.74
25 6 0.13
ACGTcount: A:0.51, C:0.20, G:0.14, T:0.15
Consensus pattern (24 bp):
TAAATGAACGAACATTAACGAACG
Found at i:108718 original size:408 final size:408
Alignment explanation
Indices: 107963--108780 Score: 1528
Period size: 408 Copynumber: 2.0 Consensus size: 408
107953 CCATGTTAAT
* *
107963 ATTGTTGGGTTTTCCAAATAAAATTAGGTTAATTATGGAGTTGGTCATTAGAATATCAGATTAAT
1 ATTGTTGGATTTTCCAAATAAAATTAGGTTAATTATGGAGTTGGTCATCAGAATATCAGATTAAT
108028 TAATATTTTTAAGATACTTACAAATTGGTCCCAAAATTGATTTAAGAAGATTGGGTTAAACATAA
66 TAATATTTTTAAGATACTTACAAATTGGTCCCAAAATTGATTTAAGAAGATTGGGTTAAACATAA
* *
108093 ATGAATGAACATAAACGAACATAACCGAACAAACATAACCAAATGAATATAATCGAACGTTCACG
131 ATGAATGAACATAAACGAACATAACCGAACAAACATAACCAAACGAATATAATCGAACATTCACG
108158 AACGTAAATGAACGAACGAGACCTATGTTCATGTCCGTTCATTTAATTAAATGAACACAAAATCT
196 AACGTAAATGAACGAACGAGACCTATGTTCATGTCCGTTCATTTAATTAAATGAACACAAAATCT
* *
108223 TGTTCATGTTCGTTCATTTAATAAATAAACGCATATAAACGAACTTCCCACCGCACGGTTCATGA
261 TGTTCATGTTCGTTCATTTAATAAATAAACGCACATAAACGAACTTCCCACCGCACGATTCATGA
*
108288 ACGGTTCGCTGAACGTTCAGTTCATTTACATGCCTAATCGAAAGTGCTGCACAGAGGTCGAATGC
326 ACGGTTCGCTGAACGTTCAGTTCATTTACAGGCCTAATCGAAAGTGCTGCACAGAGGTCGAATGC
108353 AACGAACTTGCGACCGGA
391 AACGAACTTGCGACCGGA
108371 ATTGTTGGATTTTCCAAATAAAATTAGGTTAATTATGGAGTTGGTCATCAGAATATCAGATTAAT
1 ATTGTTGGATTTTCCAAATAAAATTAGGTTAATTATGGAGTTGGTCATCAGAATATCAGATTAAT
*
108436 TAATATTTTTAAGATACTTACAACTTGGTCCCAAAATTGATTTAAGAAGATTGGGTTAAACATAA
66 TAATATTTTTAAGATACTTACAAATTGGTCCCAAAATTGATTTAAGAAGATTGGGTTAAACATAA
* *
108501 ATGAATGAACATAAACGAACATAACCGAACGAACATAACCGAACGAATATAATCGAACATTCACG
131 ATGAATGAACATAAACGAACATAACCGAACAAACATAACCAAACGAATATAATCGAACATTCACG
108566 AACGTAAATGAACGAACGAGACCTATGTTCATGTCCGTTCATTTAATTAAATGAACACAAAATCT
196 AACGTAAATGAACGAACGAGACCTATGTTCATGTCCGTTCATTTAATTAAATGAACACAAAATCT
* *
108631 TGTTCATGTTCGTTCATTTAATAAATAAACGCACATAAACGAACTTTCCGCCGCACGATTCATGA
261 TGTTCATGTTCGTTCATTTAATAAATAAACGCACATAAACGAACTTCCCACCGCACGATTCATGA
108696 ACGGTTCGCTGAACGTTCAGTTCATTTACAGGCCTAATCGAAAGTGCTGCACAGAGGTCGAATGC
326 ACGGTTCGCTGAACGTTCAGTTCATTTACAGGCCTAATCGAAAGTGCTGCACAGAGGTCGAATGC
108761 AACGAACTTGCGACCGGA
391 AACGAACTTGCGACCGGA
108779 AT
1 AT
108781 GACATTAACT
Statistics
Matches: 398, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
408 398 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.28
Consensus pattern (408 bp):
ATTGTTGGATTTTCCAAATAAAATTAGGTTAATTATGGAGTTGGTCATCAGAATATCAGATTAAT
TAATATTTTTAAGATACTTACAAATTGGTCCCAAAATTGATTTAAGAAGATTGGGTTAAACATAA
ATGAATGAACATAAACGAACATAACCGAACAAACATAACCAAACGAATATAATCGAACATTCACG
AACGTAAATGAACGAACGAGACCTATGTTCATGTCCGTTCATTTAATTAAATGAACACAAAATCT
TGTTCATGTTCGTTCATTTAATAAATAAACGCACATAAACGAACTTCCCACCGCACGATTCATGA
ACGGTTCGCTGAACGTTCAGTTCATTTACAGGCCTAATCGAAAGTGCTGCACAGAGGTCGAATGC
AACGAACTTGCGACCGGA
Found at i:115167 original size:185 final size:183
Alignment explanation
Indices: 114892--115237 Score: 568
Period size: 185 Copynumber: 1.9 Consensus size: 183
114882 TTTAAATATT
* *
114892 AAATATATTATATATAACATATGGGTTCAACCCAAACCATTTAAAACCCAATTAATATTTTAAGA
1 AAATATATTATATATAACATATGGGTTCAACCCAAACCATTTAAAACACAATTAATAATTTAAGA
** * *
114957 TTTAATAAATTTTACACGTAAATCAATATTAATTAATTA-AAAATTTTATATAAAATTTTTATTT
66 TCAAATAAATTTTAAACCTAAATCAATATTAATTAATTACAAAA--TTATAT-AAATTTTTATTT
115021 TATAATTATATATTATTTAAATTAATTATAAACTGCTTTTCTGAAATAAAAAATAA
128 TATAATTATATATTATTTAAATTAATTATAAACTGCTTTTCTGAAATAAAAAATAA
* **
115077 AAATATATTATATATAATATATGGGTTCGGCCCAAACCATTTAAAACACAATTAATAATTTAAGA
1 AAATATATTATATATAACATATGGGTTCAACCCAAACCATTTAAAACACAATTAATAATTTAAGA
*
115142 TCAAATAACTTTTAAACCTAAATCAATATTAATTAATTACAAAATTATATAAATTTTTATTTTAT
66 TCAAATAAATTTTAAACCTAAATCAATATTAATTAATTACAAAATTATATAAATTTTTATTTTAT
115207 AATTATATATTATTTAAATTAATTATAAACT
131 AATTATATATTATTTAAATTAATTATAAACT
115238 ATTTTTTTGA
Statistics
Matches: 150, Mismatches: 10, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
183 46 0.31
184 6 0.04
185 94 0.63
186 4 0.03
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.41
Consensus pattern (183 bp):
AAATATATTATATATAACATATGGGTTCAACCCAAACCATTTAAAACACAATTAATAATTTAAGA
TCAAATAAATTTTAAACCTAAATCAATATTAATTAATTACAAAATTATATAAATTTTTATTTTAT
AATTATATATTATTTAAATTAATTATAAACTGCTTTTCTGAAATAAAAAATAA
Found at i:115240 original size:20 final size:20
Alignment explanation
Indices: 115206--115263 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
115196 TTTTATTTTA
* *
115206 TAATTATATATTATTTAAAT
1 TAATTATAAAATATTTAAAT
* **
115226 TAATTATAAACTATTT-TTT
1 TAATTATAAAATATTTAAAT
115245 TGAATTATAAAATATTTAA
1 T-AATTATAAAATATTTAA
115264 TTTTTATATA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
TAATTATAAAATATTTAAAT
Found at i:115801 original size:134 final size:134
Alignment explanation
Indices: 115647--115918 Score: 535
Period size: 134 Copynumber: 2.0 Consensus size: 134
115637 ACCTTTGAAA
115647 TAGGTAACATTAAAAATATCTCGGTCATACAAATTTTATTATATCTTAGTCAAATATATTAATCT
1 TAGGTAACATTAAAAATATCTCGGTCATACAAATTTTATTATATCTTAGTCAAATATATTAATCT
115712 CCAACTTAAACGAACGCAATATTTTAACTAAAGTTTTTACTGGTAACACGACGCTTGCACTAAAG
66 CCAACTTAAACGAACGCAATATTTTAACTAAAGTTTTTACTGGTAACACGACGCTTGCACTAAAG
115777 TTTT
131 TTTT
*
115781 TAGGTAACATTAACAATATCTCGGTCATACAAATTTTATTATATCTTAGTCAAATATATTAATCT
1 TAGGTAACATTAAAAATATCTCGGTCATACAAATTTTATTATATCTTAGTCAAATATATTAATCT
115846 CCAACTTAAACGAACGCAATATTTTAACTAAAGTTTTTACTGGTAACACGACGCTTGCACTAAAG
66 CCAACTTAAACGAACGCAATATTTTAACTAAAGTTTTTACTGGTAACACGACGCTTGCACTAAAG
115911 TTTT
131 TTTT
115915 TAGG
1 TAGG
115919 ATTAAATTAT
Statistics
Matches: 137, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
134 137 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.36
Consensus pattern (134 bp):
TAGGTAACATTAAAAATATCTCGGTCATACAAATTTTATTATATCTTAGTCAAATATATTAATCT
CCAACTTAAACGAACGCAATATTTTAACTAAAGTTTTTACTGGTAACACGACGCTTGCACTAAAG
TTTT
Found at i:126750 original size:28 final size:28
Alignment explanation
Indices: 126688--126764 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 28
126678 CTTTGACGAT
*
126688 TTAACAATTCAGTGGTATAATTGAAACAA
1 TTAA-AATTCAGTGATATAATTGAAACAA
* * *
126717 TCAAAATTTAGTGCTATAATTGACAA-AA
1 TTAAAATTCAGTGATATAATTGA-AACAA
126745 TTAAAAGTTCAGTGATATAA
1 TTAAAA-TTCAGTGATATAA
126765 ACAATACAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 24 0.60
29 16 0.40
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.32
Consensus pattern (28 bp):
TTAAAATTCAGTGATATAATTGAAACAA
Found at i:130446 original size:29 final size:30
Alignment explanation
Indices: 130374--130447 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 30
130364 CAAGTTAACG
*
130374 GTTCAGTGGTATAATTGAAACGAAAATCAAA
1 GTTCAGTGGTATAATTG-AACGAAAATAAAA
* *
130405 GTTCAATGTTATAATTG-AC-AAAACTAAAA
1 GTTCAGTGGTATAATTGAACGAAAA-TAAAA
*
130434 GTTTAGTGGTATAA
1 GTTCAGTGGTATAA
130448 ACAATACATC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
28 4 0.11
29 17 0.47
31 15 0.42
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.31
Consensus pattern (30 bp):
GTTCAGTGGTATAATTGAACGAAAATAAAA
Found at i:131748 original size:35 final size:36
Alignment explanation
Indices: 131709--131788 Score: 101
Period size: 35 Copynumber: 2.2 Consensus size: 36
131699 AAAATAGTCA
* *
131709 TCAATTACACTCTAAACC-CTAAATT-CTAAAATGCT
1 TCAATTACACTCTAAACCTC-AAATTCCAAAAATACT
**
131744 TCAATTACTTTCTAAACCTCAAATTCCAAAAATACT
1 TCAATTACACTCTAAACCTCAAATTCCAAAAATACT
131780 TCAATTACA
1 TCAATTACA
131789 TGCCCAACCC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
35 21 0.55
36 17 0.45
ACGTcount: A:0.41, C:0.25, G:0.01, T:0.33
Consensus pattern (36 bp):
TCAATTACACTCTAAACCTCAAATTCCAAAAATACT
Found at i:131803 original size:36 final size:36
Alignment explanation
Indices: 131709--131805 Score: 90
Period size: 36 Copynumber: 2.7 Consensus size: 36
131699 AAAATAGTCA
* * * *
131709 TCAATTACACT-CTAAACCCTAAATT-CTAAAATGCT
1 TCAATTACA-TGCCAAACCCCAAATTCCAAAAATACT
* * * *
131744 TCAATTACTTTCTAAACCTCAAATTCCAAAAATACT
1 TCAATTACATGCCAAACCCCAAATTCCAAAAATACT
*
131780 TCAATTACATGCCCAACCCCAAATTC
1 TCAATTACATGCCAAACCCCAAATTC
131806 ATAATTCATT
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
34 1 0.02
35 20 0.40
36 29 0.58
ACGTcount: A:0.39, C:0.29, G:0.02, T:0.30
Consensus pattern (36 bp):
TCAATTACATGCCAAACCCCAAATTCCAAAAATACT
Found at i:132644 original size:35 final size:34
Alignment explanation
Indices: 132589--132683 Score: 127
Period size: 35 Copynumber: 2.7 Consensus size: 34
132579 AATGGGTTAT
* * *
132589 GAATTTGGGGTTAGACATGTAATTGAAGTATTTTG
1 GAATTTGGGTTTA-AAATGTAATTGAAGCATTTTG
*
132624 GAATTTGAGGTTTATAATGTAATTGAAGCATTTTG
1 GAATTTG-GGTTTAAAATGTAATTGAAGCATTTTG
*
132659 GATTTTGGGTTTAAAATGTAATTGA
1 GAATTTGGGTTTAAAATGTAATTGA
132684 TGATTGTATT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
34 17 0.32
35 31 0.58
36 5 0.09
ACGTcount: A:0.31, C:0.02, G:0.25, T:0.42
Consensus pattern (34 bp):
GAATTTGGGTTTAAAATGTAATTGAAGCATTTTG
Found at i:133520 original size:34 final size:36
Alignment explanation
Indices: 133456--133532 Score: 106
Period size: 35 Copynumber: 2.2 Consensus size: 36
133446 AAAACAATCA
*
133456 TCAATTACATTCTAAATCCCAAATTCT-AAAATGCT
1 TCAATTACATTCTAAATCCCAAATTCTAAAAATACT
*
133491 TCAATTACTTTCTAAA-CCTC-AATTCTAAAAATACT
1 TCAATTACATTCTAAATCC-CAAATTCTAAAAATACT
133526 TCAATTA
1 TCAATTA
133533 TATGCCCAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
34 8 0.21
35 30 0.79
ACGTcount: A:0.40, C:0.22, G:0.01, T:0.36
Consensus pattern (36 bp):
TCAATTACATTCTAAATCCCAAATTCTAAAAATACT
Found at i:134466 original size:35 final size:35
Alignment explanation
Indices: 134427--134506 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
134417 GGGGTTGGGC
* *
134427 ATGTAATTGAAGTATTTTGGAATTTGAGGTTTAGA
1 ATGTAATTGAAGTATTTTAGAATTTGAGGTTTAAA
* *
134462 ATGTAATTGAAGTATTTTAGATTTTGGGGTTTAAA
1 ATGTAATTGAAGTATTTTAGAATTTGAGGTTTAAA
134497 ATGTAATTGA
1 ATGTAATTGA
134507 TGACTATATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.44
Consensus pattern (35 bp):
ATGTAATTGAAGTATTTTAGAATTTGAGGTTTAAA
Found at i:138205 original size:67 final size:67
Alignment explanation
Indices: 138097--138226 Score: 251
Period size: 67 Copynumber: 1.9 Consensus size: 67
138087 AGAAAAAACA
138097 TCAATGAACACATTATTTTCAACCCATTGTTCATCTCAATGGGAAGTCTTCTTCTTCTTCTTCTT
1 TCAATGAACACATTATTTTCAACCCATTGTTCATCTCAATGGGAAGTCTTCTTCTTCTTCTTCTT
138162 CT
66 CT
*
138164 TCAATGAACACATTATTTTCAACCCATTGTTCATCTCAATGGGAAGTTTTCTTCTTCTTCTTC
1 TCAATGAACACATTATTTTCAACCCATTGTTCATCTCAATGGGAAGTCTTCTTCTTCTTCTTC
138227 AACAACAACA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.23, C:0.25, G:0.09, T:0.43
Consensus pattern (67 bp):
TCAATGAACACATTATTTTCAACCCATTGTTCATCTCAATGGGAAGTCTTCTTCTTCTTCTTCTT
CT
Found at i:140460 original size:16 final size:16
Alignment explanation
Indices: 140439--140471 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
140429 ATGTCTTGCC
140439 GATCCATAAATTACAT
1 GATCCATAAATTACAT
*
140455 GATCCATAAATTGCAT
1 GATCCATAAATTACAT
140471 G
1 G
140472 GTTAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.30
Consensus pattern (16 bp):
GATCCATAAATTACAT
Found at i:143858 original size:3 final size:3
Alignment explanation
Indices: 143850--143877 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
143840 TAAGACCAAA
143850 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
143878 GTAGAACTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:144337 original size:14 final size:14
Alignment explanation
Indices: 144320--144349 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
144310 AATTTAATTA
144320 TAATATATAGATAT
1 TAATATATAGATAT
*
144334 TAATATATATATAT
1 TAATATATAGATAT
144348 TA
1 TA
144350 TAAAAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
TAATATATAGATAT
Found at i:144932 original size:23 final size:23
Alignment explanation
Indices: 144906--144951 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
144896 ATGATACAAC
*
144906 ATAAATAATA-AATAATATTAATT
1 ATAAATAAAATAATAAT-TTAATT
144929 ATAAATAAAATAATAATTTAATT
1 ATAAATAAAATAATAATTTAATT
144952 TTGAAACGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
ATAAATAAAATAATAATTTAATT
Found at i:146028 original size:29 final size:31
Alignment explanation
Indices: 145995--146077 Score: 91
Period size: 29 Copynumber: 2.7 Consensus size: 31
145985 ATATAATGAT
*
145995 AGTTTGGAGATGAAATTGGAAT-A-TTCAAA
1 AGTTTGAAGATGAAATTGGAATGAGTTCAAA
* * *
146024 AGTTTGAAGATTAATTTAGAATGAGGTTCAAA
1 AGTTTGAAGATGAAATTGGAATGA-GTTCAAA
*
146056 A-TTTGAAGATGAAATTGAAATG
1 AGTTTGAAGATGAAATTGGAATG
146078 TTAAAAATTT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
29 18 0.42
30 1 0.02
31 17 0.40
32 7 0.16
ACGTcount: A:0.42, C:0.02, G:0.23, T:0.33
Consensus pattern (31 bp):
AGTTTGAAGATGAAATTGGAATGAGTTCAAA
Found at i:148697 original size:5 final size:5
Alignment explanation
Indices: 148689--148718 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
148679 AAGCAACCAC
148689 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA
148719 GAACTTTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:156017 original size:40 final size:37
Alignment explanation
Indices: 155962--156042 Score: 99
Period size: 40 Copynumber: 2.1 Consensus size: 37
155952 ATACTTGAAG
* *
155962 TTTATTTTTTATTTCATTTTAGTATCATGCCGTTAAAAA
1 TTTAGTTTTTATTTCATTTAAGTATC-T-CCGTTAAAAA
* *
156001 CTTTAGTTTTTGTTTCATTTAAGTATCTCCGTTCAAAA
1 -TTTAGTTTTTATTTCATTTAAGTATCTCCGTTAAAAA
156039 TTTA
1 TTTA
156043 ACGTTAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 4 0.11
38 9 0.24
39 1 0.03
40 23 0.62
ACGTcount: A:0.26, C:0.12, G:0.09, T:0.53
Consensus pattern (37 bp):
TTTAGTTTTTATTTCATTTAAGTATCTCCGTTAAAAA
Found at i:161058 original size:3 final size:3
Alignment explanation
Indices: 161050--161077 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
161040 TTAATTTAAA
161050 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
161078 TAACTTACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:161864 original size:352 final size:352
Alignment explanation
Indices: 161220--162276 Score: 2087
Period size: 352 Copynumber: 3.0 Consensus size: 352
161210 CGACCCAACT
161220 AAACCCTAACCTTAGGGTATCAACATCCCAGCGCCGCACCAACATAGACCATTCGATCTGGACCC
1 AAACCCTAACCTTAGGGTATCAACATCCCAGCGCCGCACCAACATAGACCATTCGATCTGGACCC
161285 ATCCAACGGTCCAGATCGATGGTAAATAGGGTTTCACAACCCTAAGCCAGTCCAGCCGTCGCGCC
66 ATCCAACGGTCCAGATCGATGGTAAATAGGGTTTCACAACCCTAAGCCAGTCCAGCCGTCGCGCC
161350 TCTTCAACGTTCCAGTAGCCGTTCAAGCCGAATATCACCGAGCCTCAAGCCACCGTCGAACCTCT
131 TCTTCAACGTTCCAGTAGCCGTTCAAGCCGAATATCACCGAGCCTCAAGCCACCGTCGAACCTCT
*
161415 CATCGAGTCAATCTATTATCCACAGTGACAACAAGGCCATCAAATACCAAATCAGTCAGAGCAAT
196 CATCGAGTCAATCTATCATCCACAGTGACAACAAGGCCATCAAATACCAAATCAGTCAGAGCAAT
161480 CAGAGAAAAATAAAGGAAAAAATCAAAAGAAAATCCAAATGATATCCTAAGGTACATCTAGCCTC
261 CAGAGAAAAATAAAGGAAAAAATCAAAAGAAAATCCAAATGATATCCTAAGGTACATCTAGCCTC
161545 TGTCGACCCTAGTGTCTCGGGCAGCAA
326 TGTCGACCCTAGTGTCTCGGGCAGCAA
161572 AAACCCTAACCTTAGGGTATCAACATCCCAGCGCCGCACCAACATAGACCATTCGATCTGGACCC
1 AAACCCTAACCTTAGGGTATCAACATCCCAGCGCCGCACCAACATAGACCATTCGATCTGGACCC
161637 ATCCAACGGTCCAGATCGATGGTAAATAGGGTTTCACAACCCTAAGCCAGTCCAGCCGTCGCGCC
66 ATCCAACGGTCCAGATCGATGGTAAATAGGGTTTCACAACCCTAAGCCAGTCCAGCCGTCGCGCC
161702 TCTTCAACGTTCCAGTAGCCGTTCAAGCCGAATATCACCGAGCCTCAAGCCACCGTCGAACCTCT
131 TCTTCAACGTTCCAGTAGCCGTTCAAGCCGAATATCACCGAGCCTCAAGCCACCGTCGAACCTCT
161767 CATCGAGTCAATCTATCATCCACAGTGACAACAAGGCCATCAAATACCAAATCAGTCAGAGCAAT
196 CATCGAGTCAATCTATCATCCACAGTGACAACAAGGCCATCAAATACCAAATCAGTCAGAGCAAT
161832 CAGAGAAAAATAAAGGAAAAAATCAAAAGAAAATCCAAATGATATCCTAAGGTACATCTAGCCTC
261 CAGAGAAAAATAAAGGAAAAAATCAAAAGAAAATCCAAATGATATCCTAAGGTACATCTAGCCTC
161897 TGTCGACCCTAGTGTCTCGGGCAGCAA
326 TGTCGACCCTAGTGTCTCGGGCAGCAA
161924 AAACCCTAACCTTAGGGTATCAACATCCCAGCGCCGCACCAACATAGACCATTCGATCTGGACCC
1 AAACCCTAACCTTAGGGTATCAACATCCCAGCGCCGCACCAACATAGACCATTCGATCTGGACCC
*
161989 ATCCAACGGTCCAAATCGATGGTAAATAGGGTTTCACAACCCTAAGCCAGTCCAGCCGTCGCGCC
66 ATCCAACGGTCCAGATCGATGGTAAATAGGGTTTCACAACCCTAAGCCAGTCCAGCCGTCGCGCC
162054 TCTTCAACGTTCCAGTAGCCGTTCAAGCCGAATATCACCGAGCCTCAAGCCACCGTCGAACCTCT
131 TCTTCAACGTTCCAGTAGCCGTTCAAGCCGAATATCACCGAGCCTCAAGCCACCGTCGAACCTCT
162119 CATCGAGTCAATCTATCATCCACAGTGACAACAAGGCCATCAAATACCAAATCAGTCAGAGCAAT
196 CATCGAGTCAATCTATCATCCACAGTGACAACAAGGCCATCAAATACCAAATCAGTCAGAGCAAT
162184 CAGAGAAAAATAAAGGAAAAAATCAAAAGAAAATCCAAATGATATCCTAAGGTACATCTAGCCTC
261 CAGAGAAAAATAAAGGAAAAAATCAAAAGAAAATCCAAATGATATCCTAAGGTACATCTAGCCTC
*
162249 TGTCGACCCTAGTGTCTTGGGCAGCAA
326 TGTCGACCCTAGTGTCTCGGGCAGCAA
162276 A
1 A
162277 GTCAATCATC
Statistics
Matches: 702, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
352 702 1.00
ACGTcount: A:0.34, C:0.30, G:0.18, T:0.19
Consensus pattern (352 bp):
AAACCCTAACCTTAGGGTATCAACATCCCAGCGCCGCACCAACATAGACCATTCGATCTGGACCC
ATCCAACGGTCCAGATCGATGGTAAATAGGGTTTCACAACCCTAAGCCAGTCCAGCCGTCGCGCC
TCTTCAACGTTCCAGTAGCCGTTCAAGCCGAATATCACCGAGCCTCAAGCCACCGTCGAACCTCT
CATCGAGTCAATCTATCATCCACAGTGACAACAAGGCCATCAAATACCAAATCAGTCAGAGCAAT
CAGAGAAAAATAAAGGAAAAAATCAAAAGAAAATCCAAATGATATCCTAAGGTACATCTAGCCTC
TGTCGACCCTAGTGTCTCGGGCAGCAA
Found at i:163017 original size:19 final size:19
Alignment explanation
Indices: 162971--163017 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
162961 CATTAATTTG
*
162971 TATATTATGTTTGCTGATAT
1 TATATT-TGGTTGCTGATAT
162991 TATAATTTGGTTG-TGATATT
1 TAT-ATTTGGTTGCTGATA-T
163011 TATATTT
1 TATATTT
163018 ATTTCGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 9 0.38
20 12 0.50
21 3 0.12
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (19 bp):
TATATTTGGTTGCTGATAT
Found at i:171603 original size:21 final size:21
Alignment explanation
Indices: 171574--171626 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
171564 ACGCGATCTC
*
171574 CATTATCGCAAATTCGCGTTG
1 CATTTTCGCAAATTCGCGTTG
171595 CATTTTCGCAAATTCGCGTTG
1 CATTTTCGCAAATTCGCGTTG
171616 CATTTTCGCAA
1 CATTTTCGCAA
171627 TGCGATAGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.36
Consensus pattern (21 bp):
CATTTTCGCAAATTCGCGTTG
Found at i:171709 original size:20 final size:21
Alignment explanation
Indices: 171684--171735 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
171674 TTTTCCCAAT
*
171684 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
171704 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
171725 TCGCAATGCGA
1 TCGCAATGCGA
171736 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:171749 original size:20 final size:20
Alignment explanation
Indices: 171724--171831 Score: 110
Period size: 20 Copynumber: 5.3 Consensus size: 20
171714 AATTGGGAAA
171724 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
171744 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
171764 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
171785 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
171805 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
*
171825 TTCGCAA
1 ATCGCAA
171832 CGTGATTTAC
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.03
20 58 0.77
21 13 0.17
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:171832 original size:20 final size:20
Alignment explanation
Indices: 171786--171838 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
171776 TAATACAAAA
*
171786 TCGCAACGAGATACTGACTT
1 TCGCAACGAGATTCTGACTT
*
171806 TCGCAACGCGATTCTGACTT
1 TCGCAACGAGATTCTGACTT
*
171826 TCGCAACGTGATT
1 TCGCAACGAGATT
171839 TACATAGCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (20 bp):
TCGCAACGAGATTCTGACTT
Found at i:172394 original size:19 final size:19
Alignment explanation
Indices: 172356--172423 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
172346 TTCGAGAATG
172356 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
172376 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
172395 AAAATTCGCAACGCGAAACC
1 AAAA-TCGCAACGCGAAATA
172415 AAAATCGCA
1 AAAATCGCA
172424 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 13 0.32
20 28 0.68
ACGTcount: A:0.47, C:0.25, G:0.16, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:172465 original size:20 final size:20
Alignment explanation
Indices: 172419--172489 Score: 103
Period size: 19 Copynumber: 3.7 Consensus size: 20
172409 GAAACCAAAA
172419 TCGCA-TTGCGATTTTCATT
1 TCGCAGTTGCGATTTTCATT
* *
172438 TCG-TGTTGCGATTTTTATT
1 TCGCAGTTGCGATTTTCATT
172457 TCGCAGTTGCGATTTTCATT
1 TCGCAGTTGCGATTTTCATT
172477 TCGC-GTTGCGATT
1 TCGCAGTTGCGATT
172490 GTCTGGTCGC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 28 0.61
20 18 0.39
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.48
Consensus pattern (20 bp):
TCGCAGTTGCGATTTTCATT
Found at i:172509 original size:33 final size:33
Alignment explanation
Indices: 172472--172559 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
172462 GTTGCGATTT
* *
172472 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
172505 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
172538 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
172560 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:172561 original size:20 final size:20
Alignment explanation
Indices: 172527--172584 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
172517 GCGATTCTCT
**
172527 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
172547 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
172567 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
172585 AACAAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:174663 original size:21 final size:21
Alignment explanation
Indices: 174639--174705 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
174629 TCATTCCTCG
174639 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
174660 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
174681 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
174702 AGAG
1 AGAG
174706 CCCAATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:174663 original size:42 final size:42
Alignment explanation
Indices: 174583--174705 Score: 106
Period size: 42 Copynumber: 2.9 Consensus size: 42
174573 GCCCGACTCG
* * ** * * *
174583 CCTATCATCCCTCAAGAGTCTACTCCTATCGTTGAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
174625 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
* * * * *
174667 ACTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
174706 CCCAATTCAC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 61 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.24
Consensus pattern (42 bp):
CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
Found at i:176084 original size:14 final size:14
Alignment explanation
Indices: 176065--176100 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
176055 TTTGTTTAAT
176065 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
176079 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
176093 TGATTTGT
1 TGATTTGT
176101 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:176306 original size:33 final size:32
Alignment explanation
Indices: 176264--176389 Score: 191
Period size: 33 Copynumber: 3.8 Consensus size: 32
176254 TTAAATTCGT
176264 GTTGCGATTTTCATTTCGCATTGCGATTCCCTC
1 GTTGCGATTTTCATTTCGCATTGCGATT-CCTC
**
176297 GTTGCGATTTTCATTTCGCATTGCGAAATT-AGC
1 GTTGCGATTTTCATTTCGCATTGCG--ATTCCTC
176330 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCATTGCGATTC-CTC
176363 GTTGCGATTTTCATTTCGCATTGCGAT
1 GTTGCGATTTTCATTTCGCATTGCGAT
176390 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
GTTGCGATTTTCATTTCGCATTGCGATTCCTC
Found at i:176348 original size:66 final size:66
Alignment explanation
Indices: 176264--176388 Score: 241
Period size: 66 Copynumber: 1.9 Consensus size: 66
176254 TTAAATTCGT
176264 GTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAAATTAG
1 GTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAAATTAG
176329 C
66 C
*
176330 GTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGA
1 GTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGA
176389 TAGTAATTTC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.42
Consensus pattern (66 bp):
GTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAAATTAG
C
Found at i:180046 original size:20 final size:20
Alignment explanation
Indices: 179989--180037 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
179979 ATTCATTTGA
179989 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
180009 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
180029 TTATCGCAA
1 CTATCGCAA
180038 TGAGAAAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.18
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:180106 original size:19 final size:19
Alignment explanation
Indices: 180065--180132 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
180055 GAAATGAAAA
180065 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
180081 TC-C-TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
180098 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
180117 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
180133 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 30 0.64
ACGTcount: A:0.13, C:0.24, G:0.16, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:182184 original size:19 final size:20
Alignment explanation
Indices: 182141--182196 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
182131 TCACAACGCA
*
182141 AAATGACTATCGTAACGCGG
1 AAATGACTATCGCAACGCGG
* *
182161 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
182180 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
182197 ACAAAATCGC
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:182204 original size:14 final size:14
Alignment explanation
Indices: 182185--182242 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
182175 ATGCGAAATG
182185 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
182199 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
182215 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
182231 AAAATCGCAACG
1 AAAATCGCAACG
182243 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:182227 original size:32 final size:33
Alignment explanation
Indices: 182169--182247 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
182159 GGAAATGGCT
*
182169 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
182202 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
182234 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
182248 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:182794 original size:18 final size:18
Alignment explanation
Indices: 182768--182812 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
182758 GTCGATCAGA
*
182768 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
182786 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
182804 TGATGGCTC
1 TGATGGCTC
182813 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:184157 original size:20 final size:20
Alignment explanation
Indices: 184132--184205 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
184122 AATAGTTTCT
184132 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
184152 GAAAATGACTATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
184172 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
*
184192 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
184206 GTTGCGATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
19 6 0.12
20 42 0.88
ACGTcount: A:0.47, C:0.23, G:0.16, T:0.14
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:184466 original size:22 final size:22
Alignment explanation
Indices: 184439--184482 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
184429 GATGGAGATA
184439 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
184461 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
184483 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:184695 original size:20 final size:20
Alignment explanation
Indices: 184670--184722 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
184660 GATTATGTAT
*
184670 TATCGCGTTGCGAAAGTTAG
1 TATCGCGTTGCGAAAGTAAG
184690 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
184710 TATCTCGTTGCGA
1 TATCGCGTTGCGA
184723 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:184777 original size:20 final size:20
Alignment explanation
Indices: 184733--184825 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
184723 TTTTTTATTA
* **
184733 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
184754 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
184774 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
184795 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
184815 TCGCATTGCGA
1 TCGCATTGCGA
184826 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:184778 original size:41 final size:41
Alignment explanation
Indices: 184715--184825 Score: 188
Period size: 41 Copynumber: 2.7 Consensus size: 41
184705 GTAAGTATCT
*
184715 CGTTGCGATTT-TTTATTATCGCATTGCGATTTTCCCAATTCG
1 CGTTGCGATTTACTTA-T-TCGCATTGCGATTTTCCCAATTCG
184757 CGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCG
1 CGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCG
184798 CGTTGCGATTTACTTATTCGCATTGCGA
1 CGTTGCGATTTACTTATTCGCATTGCGA
184826 ATTGGGAAAA
Statistics
Matches: 67, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
41 52 0.78
42 12 0.18
43 3 0.04
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (41 bp):
CGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCG
Found at i:186410 original size:14 final size:14
Alignment explanation
Indices: 186391--186424 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
186381 GCTAAACCAG
186391 AAATGCAGCAACGT
1 AAATGCAGCAACGT
186405 AAATGCAGCAACGT
1 AAATGCAGCAACGT
*
186419 GAATGC
1 AAATGC
186425 GATGAAGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.41, C:0.21, G:0.24, T:0.15
Consensus pattern (14 bp):
AAATGCAGCAACGT
Found at i:196563 original size:21 final size:21
Alignment explanation
Indices: 196512--196564 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
196502 ATTATGACTA
196512 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
***
196533 TCGTGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
196554 TCGCAATGCGA
1 TCGCAATGCGA
196565 ATTTGGAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:196645 original size:18 final size:18
Alignment explanation
Indices: 196624--196682 Score: 82
Period size: 18 Copynumber: 3.2 Consensus size: 18
196614 AATTGCAATG
196624 CGATACTGACTTTCGCAA
1 CGATACTGACTTTCGCAA
*
196642 CGATACTTACTTTCGCAACA
1 CGATACTGACTTTCGC-A-A
*
196662 CGATACTGCCTTTCGCAA
1 CGATACTGACTTTCGCAA
196680 CGA
1 CGA
196683 GATAATACAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 19 0.53
19 2 0.06
20 15 0.42
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (18 bp):
CGATACTGACTTTCGCAA
Found at i:196666 original size:20 final size:20
Alignment explanation
Indices: 196624--196680 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
196614 AATTGCAATG
196624 CGATACTGACTTTCGC-A-A
1 CGATACTGACTTTCGCAACA
*
196642 CGATACTTACTTTCGCAACA
1 CGATACTGACTTTCGCAACA
*
196662 CGATACTGCCTTTCGCAAC
1 CGATACTGACTTTCGCAAC
196681 GAGATAATAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
18 15 0.44
19 1 0.03
20 18 0.53
ACGTcount: A:0.26, C:0.32, G:0.14, T:0.28
Consensus pattern (20 bp):
CGATACTGACTTTCGCAACA
Found at i:196899 original size:22 final size:22
Alignment explanation
Indices: 196873--196916 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
196863 CACTCTCTCA
*
196873 CCCATCTTCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
196895 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
196917 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:197226 original size:20 final size:20
Alignment explanation
Indices: 197177--197235 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
197167 TTTATTCTCT
* **
197177 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
197197 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
197217 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
197236 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:197426 original size:25 final size:24
Alignment explanation
Indices: 197372--197426 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
197362 TGTTTATTAT
* *
197372 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
197396 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
197422 TGTTT
1 TGTTT
197427 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:198110 original size:14 final size:14
Alignment explanation
Indices: 198076--198114 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
198066 TTGATTGTTT
198076 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
198090 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
198104 TGTTGATTTGT
1 AATTGATTTGT
198115 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:198376 original size:20 final size:20
Alignment explanation
Indices: 198318--198378 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
198308 TCGCGTTGCA
* *
198318 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGTC
*
198338 ATTTTCGTGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGTC
198358 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGTC
198378 A
1 A
198379 AATGAATGTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGTC
Found at i:198927 original size:20 final size:20
Alignment explanation
Indices: 198902--198953 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
198892 ATTTTGTATT
* * *
198902 ATCTCGTTGGGATAGTTAGA
1 ATCTCGTTGCGAAAGTCAGA
198922 ATCTCGTTGCGAAAGTCAGA
1 ATCTCGTTGCGAAAGTCAGA
*
198942 ATCGCGTTGCGA
1 ATCTCGTTGCGA
198954 TTTTGTATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (20 bp):
ATCTCGTTGCGAAAGTCAGA
Found at i:199017 original size:61 final size:61
Alignment explanation
Indices: 198880--198993 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 61
198870 GAACTTTGAA
* * * *
198880 AATCGCATTGCGATTTTGTATTATCTCGTTGGGATAGTTAGAATCTCGTTGCGAAAGTCAG
1 AATCGCATTGCGATTTTGTATTATCTCGTTGCGATAGTCAGAATCGCATTGCGAAAGTCAG
* *
198941 AATCGCGTTGCGATTTTGTA-TATCGT-GTTGCGATAGTCAGTATCGCATTGCGA
1 AATCGCATTGCGATTTTGTATTATC-TCGTTGCGATAGTCAGAATCGCATTGCGA
198994 TTTTCCAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
60 26 0.57
61 20 0.43
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (61 bp):
AATCGCATTGCGATTTTGTATTATCTCGTTGCGATAGTCAGAATCGCATTGCGAAAGTCAG
Found at i:199027 original size:20 final size:21
Alignment explanation
Indices: 198983--199034 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
198973 ATAGTCAGTA
*
198983 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
199004 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
199024 TCGCATTGCGA
1 TCGCATTGCGA
199035 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:199076 original size:21 final size:22
Alignment explanation
Indices: 199024--199076 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
199014 ATTTACTTAT
199024 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
199045 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
199066 TCGCATTGCGA
1 TCGCATTGCGA
199077 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Done.