Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008460.1 Hibiscus syriacus cultivar Beakdansim tig00111273_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: 2854393
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 15
Found at i:2495018 original size:3 final size:3
Alignment explanation
Indices: 2495010--2495052 Score: 77
Period size: 3 Copynumber: 14.0 Consensus size: 3
2495000 AAATTTAAAT
2495010 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
2495053 AATATTACAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2495900 original size:17 final size:17
Alignment explanation
Indices: 2495868--2495900 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2495858 TCTCGTTTTT
2495868 AGAGAGAAATGAAGAAA
1 AGAGAGAAATGAAGAAA
2495885 AGAG-GAAATGAGAGAA
1 AGAGAGAAATGA-AGAA
2495901 TGGCCCGGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.61, C:0.00, G:0.33, T:0.06
Consensus pattern (17 bp):
AGAGAGAAATGAAGAAA
Found at i:2496680 original size:17 final size:19
Alignment explanation
Indices: 2496644--2496680 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
2496634 CATGAAATAC
2496644 AATATTATAATTTTATAAT
1 AATATTATAATTTTATAAT
*
2496663 AATATT-TATTTTTA-AAT
1 AATATTATAATTTTATAAT
2496680 A
1 A
2496681 TCAAAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 4 0.24
18 7 0.41
19 6 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AATATTATAATTTTATAAT
Found at i:2497021 original size:2 final size:2
Alignment explanation
Indices: 2497014--2497048 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2497004 ATAAATATCT
2497014 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2497049 TTTCTTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2502411 original size:13 final size:13
Alignment explanation
Indices: 2502393--2502419 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2502383 AAATAATTTA
2502393 AGGATAAATTTGT
1 AGGATAAATTTGT
2502406 AGGATAAATTTGT
1 AGGATAAATTTGT
2502419 A
1 A
2502420 ATTTAACCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (13 bp):
AGGATAAATTTGT
Found at i:2503728 original size:28 final size:28
Alignment explanation
Indices: 2503653--2503710 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
2503643 ACATAACTTT
2503653 TAGATGGTAAAAATCTGAAAATCTAGAC
1 TAGATGGTAAAAATCTGAAAATCTAGAC
2503681 TAGATGGTAAAAATCTGAAAATCTAGAC
1 TAGATGGTAAAAATCTGAAAATCTAGAC
2503709 TA
1 TA
2503711 ACTTGTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.26
Consensus pattern (28 bp):
TAGATGGTAAAAATCTGAAAATCTAGAC
Found at i:2508275 original size:18 final size:18
Alignment explanation
Indices: 2508244--2508278 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2508234 TTTAAATTTT
**
2508244 AAATTAAATTTTAAAATC
1 AAATTAAACATTAAAATC
2508262 AAATTAAACATTAAAAT
1 AAATTAAACATTAAAAT
2508279 TTATGTTCAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATTAAACATTAAAATC
Found at i:2530362 original size:31 final size:31
Alignment explanation
Indices: 2530324--2530406 Score: 139
Period size: 31 Copynumber: 2.7 Consensus size: 31
2530314 AGGGTCGAGG
2530324 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2530355 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
2530386 GATTACCTAGGTTCTTTGGGA
1 GTTTACCTATGTTCTTCGGGA
2530407 TAATTATACG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:2532589 original size:69 final size:69
Alignment explanation
Indices: 2532468--2532608 Score: 176
Period size: 69 Copynumber: 2.0 Consensus size: 69
2532458 CTTCTCCTAG
* *
2532468 AACATACCTTTTATTTCGGATAGGATAGAACACTATGAAATAACATAGATTCTCTAAATAATAAT
1 AACATACCTTTCATTTCGGATAGGATAGAACACTATGAAATAACAGAGATTCTCTAAATAATAAT
2532533 AAAA
66 AAAA
* * * * * * *
2532537 AACATCCCTTTCATTTTGGAT-GGAATTGAATACTATGACATGACAGAGATTCTCTGAATAATAA
1 AACATACCTTTCATTTCGGATAGG-ATAGAACACTATGAAATAACAGAGATTCTCTAAATAATAA
*
2532601 TAGAA
65 TAAAA
2532606 AAC
1 AAC
2532609 GCTTCCTCTG
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
68 2 0.03
69 59 0.97
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (69 bp):
AACATACCTTTCATTTCGGATAGGATAGAACACTATGAAATAACAGAGATTCTCTAAATAATAAT
AAAA
Found at i:2532664 original size:83 final size:83
Alignment explanation
Indices: 2532544--2533021 Score: 592
Period size: 83 Copynumber: 5.8 Consensus size: 83
2532534 AAAAACATCC
* * * *
2532544 CTTTCATTTTGGATGGAATTGAATACTATGACATGACAGAGATTCTCTGAATAATAATAGAAAAC
1 CTTTCATTTCGGATGGGATTGAACACTATGACATGACAGAGATTCTCTGAATAATAATGGAAAAC
* *
2532609 GCTTCCTCTGGAATGTGT
66 GCTTCCCCTGGAATGTGA
* * *
2532627 CGTTCATTTTAGG-TGGGATTGAACACTATGACATGACAGAGATTCTTTGAATAAT-ATGGAAAA
1 CTTTCA-TTTCGGATGGGATTGAACACTATGACATGACAGAGATTCTCTGAATAATAATGGAAAA
* *
2532690 CACTTCCCCTGGAACGT-A
65 CGCTTCCCCTGGAATGTGA
* * * *
2532708 CATTTCATTTCGGATGAGATAGAACACTATGACATAATAGAGATTCTCTGAATAATAATGGAAAA
1 C-TTTCATTTCGGATGGGATTGAACACTATGACATGACAGAGATTCTCTGAATAATAATGGAAAA
* ** *
2532773 CACTTCCCCTATAACGTGA
65 CGCTTCCCCTGGAATGTGA
* * *
2532792 CTTTCATTTCGGATGTGATT-ATACACTATGACATGATAGAGATTCTCTGAATAATAATGCAAAA
1 CTTTCATTTCGGATGGGATTGA-ACACTATGACATGACAGAGATTCTCTGAATAATAATGGAAAA
* * *
2532856 TGCTTCCTCTGGAATGTGT
65 CGCTTCCCCTGGAATGTGA
* *
2532875 CTTTCATTTCAGAT-GG-TTGGAACACTATGACATGACAGAGATTCCCTGAATAATAATGGAAAA
1 CTTTCATTTCGGATGGGATT-GAACACTATGACATGACAGAGATTCTCTGAATAATAATGGAAAA
* *
2532938 TGCTTCCCCTGGAATG-CA
65 CGCTTCCCCTGGAATGTGA
*
2532956 CCTTTCATTTCGGATGGGATGGAACACTATGACATGACAGAGATTCTCTGAATAATAATGGAAAA
1 -CTTTCATTTCGGATGGGATTGAACACTATGACATGACAGAGATTCTCTGAATAATAATGGAAAA
2533021 C
65 C
2533022 ACTATGACAT
Statistics
Matches: 342, Mismatches: 42, Indels: 22
0.84 0.10 0.05
Matches are distributed among these distances:
81 8 0.02
82 131 0.38
83 195 0.57
84 8 0.02
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (83 bp):
CTTTCATTTCGGATGGGATTGAACACTATGACATGACAGAGATTCTCTGAATAATAATGGAAAAC
GCTTCCCCTGGAATGTGA
Found at i:2532820 original size:165 final size:163
Alignment explanation
Indices: 2532544--2533024 Score: 583
Period size: 165 Copynumber: 2.9 Consensus size: 163
2532534 AAAAACATCC
* * * *
2532544 CTTTCATTTTGGATGGAATTGAATACTATGACATGACAGAGATTCTCTGAATAATAATAGAAAAC
1 CTTTCATTTCGGATGG-ATAGAACACTATGACATGACAGAGATTCTCTGAATAATAATGGAAAAC
* * * *
2532609 GCTTCCTCTGGAATGTGTCGTTCATTTTAGG-TGGGATTGAACACTATGACATGACAGAGATTCT
65 GCTTCCCCTGGAA-GTGACTTTCA-TTTCGGATGGGATT-AACACTATGACATGACAGAGATTCT
*
2532673 TTGAATAAT-ATGGAAAACACTTCCCCTGGAACGT-A
127 CTGAATAATAATGGAAAACACTTCCCCTGGAACGTGA
* *
2532708 CATTTCATTTCGGATGAGATAGAACACTATGACATAATAGAGATTCTCTGAATAATAATGGAAAA
1 C-TTTCATTTCGGATG-GATAGAACACTATGACATGACAGAGATTCTCTGAATAATAATGGAAAA
* ** * *
2532773 CACTTCCCCTATAACGTGACTTTCATTTCGGATGTGATTATACACTATGACATGATAGAGATTCT
64 CGCTTCCCCTGGAA-GTGACTTTCATTTCGGATGGGATTA-ACACTATGACATGACAGAGATTCT
* ** * * *
2532838 CTGAATAATAATGCAAAATGCTTCCTCTGGAATGTGT
127 CTGAATAATAATGGAAAACACTTCCCCTGGAACGTGA
* * * * *
2532875 CTTTCATTTCAGATGGTTGGAACACTATGACATGACAGAGATTCCCTGAATAATAATGGAAAATG
1 CTTTCATTTCGGATGGATAGAACACTATGACATGACAGAGATTCTCTGAATAATAATGGAAAACG
*
2532940 CTTCCCCTGGAA-TGCACCTTTCATTTCGGATGGGATGGAACACTATGACATGACAGAGATTCTC
66 CTTCCCCTGGAAGTG-A-CTTTCATTTCGGATGGGAT-TAACACTATGACATGACAGAGATTCTC
2533004 TGAATAATAATGGAAAACACT
128 TGAATAATAATGGAAAACACT
2533025 ATGACATTAC
Statistics
Matches: 269, Mismatches: 39, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
163 2 0.01
164 8 0.03
165 223 0.83
166 35 0.13
167 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (163 bp):
CTTTCATTTCGGATGGATAGAACACTATGACATGACAGAGATTCTCTGAATAATAATGGAAAACG
CTTCCCCTGGAAGTGACTTTCATTTCGGATGGGATTAACACTATGACATGACAGAGATTCTCTGA
ATAATAATGGAAAACACTTCCCCTGGAACGTGA
Found at i:2532983 original size:248 final size:248
Alignment explanation
Indices: 2532568--2533024 Score: 722
Period size: 248 Copynumber: 1.8 Consensus size: 248
2532558 GGAATTGAAT
2532568 ACTATGACATGACAGAGATTCTCTGAATAATAATAGAAAACGCTTCCTCTGGAATGTGTCGTTCA
1 ACTATGACATGACAGAGATTCTCTGAATAATAATAGAAAACGCTTCCTCTGGAATGTGTCGTTCA
* * **
2532633 TTTTAGGTGGGATTGAACACTATGACATGACAGAGATTCTTTGAATAATATGGAAAACACTTCCC
66 TTTCAGATGGGATTGAACACTATGACATGACAGAGATTCCCTGAATAATATGGAAAACACTTCCC
* *
2532698 CTGGAACGTACATTTCATTTCGGATGAGATAGAACACTATGACATAATAGAGATTCTCTGAATAA
131 CTGGAACGCACATTTCATTTCGGATGAGATAGAACACTATGACATAACAGAGATTCTCTGAATAA
2532763 TAATGGAAAACACTTCCCCTATAACGTGACTTTCATTTCGGATGTGATTATAC
196 TAATGGAAAACACTTCCCCTATAACGTGACTTTCATTTCGGATGTGATTATAC
* * *
2532816 ACTATGACATGATAGAGATTCTCTGAATAATAAT-GCAAAATGCTTCCTCTGGAATGTGTCTTTC
1 ACTATGACATGACAGAGATTCTCTGAATAATAATAG-AAAACGCTTCCTCTGGAATGTGTCGTTC
**
2532880 ATTTCAGAT-GG-TTGGAACACTATGACATGACAGAGATTCCCTGAATAATAATGGAAAATGCTT
65 ATTTCAGATGGGATT-GAACACTATGACATGACAGAGATTCCCTGAATAAT-ATGGAAAACACTT
* * * * *
2532943 CCCCTGGAATGCACCTTTCATTTCGGATGGGATGGAACACTATGACATGACAGAGATTCTCTGAA
128 CCCCTGGAACGCACATTTCATTTCGGATGAGATAGAACACTATGACATAACAGAGATTCTCTGAA
2533008 TAATAATGGAAAACACT
193 TAATAATGGAAAACACT
2533025 ATGACATTAC
Statistics
Matches: 190, Mismatches: 16, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
246 2 0.01
247 36 0.19
248 152 0.80
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (248 bp):
ACTATGACATGACAGAGATTCTCTGAATAATAATAGAAAACGCTTCCTCTGGAATGTGTCGTTCA
TTTCAGATGGGATTGAACACTATGACATGACAGAGATTCCCTGAATAATATGGAAAACACTTCCC
CTGGAACGCACATTTCATTTCGGATGAGATAGAACACTATGACATAACAGAGATTCTCTGAATAA
TAATGGAAAACACTTCCCCTATAACGTGACTTTCATTTCGGATGTGATTATAC
Found at i:2535262 original size:42 final size:42
Alignment explanation
Indices: 2535199--2535288 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 42
2535189 CAAATAGTGA
* ** * ** *
2535199 TGGCATTTGAACCGATGGATATGGCATATGGACTTGCGGATG
1 TGGCATTTAAACCGACAGATATGACATATAAACTTGCAGATG
*
2535241 TGGCATTTAAACCGACAGATATGACATCTAAACTTGCAGATG
1 TGGCATTTAAACCGACAGATATGACATATAAACTTGCAGATG
2535283 TGGCAT
1 TGGCAT
2535289 CTGAACCGGC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.28
Consensus pattern (42 bp):
TGGCATTTAAACCGACAGATATGACATATAAACTTGCAGATG
Found at i:2536956 original size:19 final size:19
Alignment explanation
Indices: 2536923--2536992 Score: 54
Period size: 19 Copynumber: 3.7 Consensus size: 19
2536913 TAAATTCAAA
* *
2536923 TAAATAAAATCTAATAATT
1 TAAATAATATATAATAATT
*
2536942 TAAATAATATATAATTGATT
1 TAAATAATATATAA-TAATT
* *
2536962 T-CATAATAT-TCATAAATT
1 TAAATAATATATAAT-AATT
*
2536980 TAAAAAATATATA
1 TAAATAATATATA
2536993 GTTTTGTATT
Statistics
Matches: 38, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
17 1 0.03
18 6 0.16
19 25 0.66
20 6 0.16
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (19 bp):
TAAATAATATATAATAATT
Found at i:2537167 original size:38 final size:37
Alignment explanation
Indices: 2537125--2537202 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 37
2537115 TAAATAATCA
*
2537125 AATAAAAATACTAA-A-ATAAAATAATTAATTACTTAAAT
1 AATAAAAA-ACTAATATATAAAA-AATTAATTA-TAAAAT
*
2537163 AATAAAAAATTAATATATAAAAAATTAATTATAAAAT
1 AATAAAAAACTAATATATAAAAAATTAATTATAAAAT
2537200 AAT
1 AAT
2537203 TATATCTTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
37 12 0.33
38 18 0.50
39 6 0.17
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (37 bp):
AATAAAAAACTAATATATAAAAAATTAATTATAAAAT
Found at i:2537182 original size:15 final size:15
Alignment explanation
Indices: 2537160--2537204 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
2537150 TAATTACTTA
2537160 AATA-ATAAAAAATT
1 AATATATAAAAAATT
2537174 AATATATAAAAAATT
1 AATATATAAAAAATT
2537189 AAT-TATAAAATAATT
1 AATATATAAAA-AATT
2537204 A
1 A
2537205 TATCTTACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AATATATAAAAAATT
Found at i:2538426 original size:16 final size:15
Alignment explanation
Indices: 2538405--2538447 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
2538395 TAGGACTTTA
2538405 TTTATTTTGATTTTC
1 TTTATTTTGATTTTC
*
2538420 TTTTATTTTAATTTTC
1 -TTTATTTTGATTTTC
*
2538436 CTTA-TTTGATTT
1 TTTATTTTGATTT
2538448 AGACTCATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 7 0.29
15 3 0.12
16 14 0.58
ACGTcount: A:0.16, C:0.07, G:0.05, T:0.72
Consensus pattern (15 bp):
TTTATTTTGATTTTC
Found at i:2538745 original size:37 final size:37
Alignment explanation
Indices: 2538692--2538796 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
2538682 CATTTTCGTC
2538692 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
2538729 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
2538766 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
2538797 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:2539193 original size:18 final size:17
Alignment explanation
Indices: 2539161--2539194 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2539151 GGATATTTTA
*
2539161 TTCATTTATTTTTATTT
1 TTCATTTATTATTATTT
2539178 TTCATGTTATTATTATT
1 TTCAT-TTATTATTATT
2539195 ATATGTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.71
Consensus pattern (17 bp):
TTCATTTATTATTATTT
Found at i:2540225 original size:20 final size:20
Alignment explanation
Indices: 2540151--2540341 Score: 201
Period size: 20 Copynumber: 9.6 Consensus size: 20
2540141 GATTTTCCAT
* ** *
2540151 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
2540171 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
2540191 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2540211 AATCGCAACGTGTATCCGT-
1 AATCGCAACGCGTATCCGTA
**
2540230 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
2540250 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2540270 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
2540290 AATCGCAACG-ATAATACATAA
1 AATCGCAACGCGT-ATCCGT-A
2540311 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2540331 AATCGC-ACGCG
1 AATCGCAACGCG
2540342 ATATTTAAAG
Statistics
Matches: 142, Mismatches: 23, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
19 23 0.16
20 101 0.71
21 17 0.12
22 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:2540239 original size:59 final size:60
Alignment explanation
Indices: 2540151--2540341 Score: 233
Period size: 59 Copynumber: 3.2 Consensus size: 60
2540141 GATTTTCCAT
* ** * *
2540151 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
2540211 AATCGCAACGTGTATCCGT-AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
2540270 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
2540331 AATCGC-ACGCG
1 AATCGCAACGCG
2540342 ATATTTAAAG
Statistics
Matches: 108, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
59 51 0.47
60 32 0.30
61 25 0.23
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:2540239 original size:79 final size:79
Alignment explanation
Indices: 2540150--2540299 Score: 212
Period size: 79 Copynumber: 1.9 Consensus size: 79
2540140 CGATTTTCCA
*
2540150 TAATCGCAACGCGAATATGAAAATCGCAACGCG-AACACATAAATCGCAACGCGTATCCGTAAAT
1 TAATCGCAACGCGAATAGGAAAATCGCAACGCGTAAC-CATAAATCGCAACGCGTATCCGTAAAT
2540214 CGCAACGTGTATCCG
65 CGCAACGTGTATCCG
* * * * * * *
2540229 TAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTATATCGCAACGCGTATCCGTAAATC
1 TAATCGCAACGCGAATAGGAAAATCGCAACGCGTAACCATAAATCGCAACGCGTATCCGTAAATC
2540294 GCAACG
66 GCAACG
2540300 ATAATACATA
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
79 60 0.97
80 2 0.03
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (79 bp):
TAATCGCAACGCGAATAGGAAAATCGCAACGCGTAACCATAAATCGCAACGCGTATCCGTAAATC
GCAACGTGTATCCG
Found at i:2540756 original size:33 final size:33
Alignment explanation
Indices: 2540717--2540787 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
2540707 TTCACTTAGA
*
2540717 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
2540750 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
2540783 TTTCA
1 TTTCA
2540788 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:2540927 original size:14 final size:14
Alignment explanation
Indices: 2540908--2540961 Score: 63
Period size: 14 Copynumber: 3.6 Consensus size: 14
2540898 AGAATGACTG
2540908 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
2540922 TCGCAACGCGAAATGAAA
1 TCGCAA--CGAGA-G-AA
2540940 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
2540954 TCGCAACG
1 TCGCAACG
2540962 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 8 0.24
17 1 0.03
18 8 0.24
ACGTcount: A:0.41, C:0.24, G:0.26, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:2540943 original size:18 final size:16
Alignment explanation
Indices: 2540918--2540966 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
2540908 TCGCAACGAG
2540918 AGAATCGCAACGCGAA
1 AGAATCGCAACGCGAA
*
2540934 ATGAAATCGCAA--CGAG
1 A-G-AATCGCAACGCGAA
2540950 AGAATCGCAACGCGAA
1 AGAATCGCAACGCGAA
2540966 A
1 A
2540967 CCAAAATCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.30
15 1 0.04
16 9 0.33
17 1 0.04
18 8 0.30
ACGTcount: A:0.45, C:0.22, G:0.24, T:0.08
Consensus pattern (16 bp):
AGAATCGCAACGCGAA
Found at i:2540995 original size:19 final size:19
Alignment explanation
Indices: 2540973--2541070 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
2540963 GAAACCAAAA
*
2540973 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2540992 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2541006 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2541025 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
2541039 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
2541058 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2541071 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2541014 original size:14 final size:14
Alignment explanation
Indices: 2540995--2541084 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
2540985 TTTCATTTCG
2540995 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2541009 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2541028 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2541042 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
2541059 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
2541075 CGTTGCGATT
1 CGTTGCGATT
2541085 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2541020 original size:33 final size:33
Alignment explanation
Indices: 2540978--2541092 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
2540968 CAAAATCGCA
2540978 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2541011 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
2541044 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2541077 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2541093 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2542494 original size:55 final size:57
Alignment explanation
Indices: 2542429--2542541 Score: 212
Period size: 55 Copynumber: 2.0 Consensus size: 57
2542419 CATCGAGCCT
2542429 CTTCTCCACCATCACCTCATGATAGGCG-CCGGC-AAGATGCCACGACTCCTATCTC
1 CTTCTCCACCATCACCTCATGATAGGCGACCGGCAAAGATGCCACGACTCCTATCTC
2542484 CTTCTCCACCATCACCTCATGATAGGCGACCGGCAAAGATGCCACGACTCCTATCTC
1 CTTCTCCACCATCACCTCATGATAGGCGACCGGCAAAGATGCCACGACTCCTATCTC
2542541 C
1 C
2542542 CTGTTCTCCA
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
55 28 0.50
56 5 0.09
57 23 0.41
ACGTcount: A:0.23, C:0.40, G:0.16, T:0.21
Consensus pattern (57 bp):
CTTCTCCACCATCACCTCATGATAGGCGACCGGCAAAGATGCCACGACTCCTATCTC
Found at i:2543024 original size:91 final size:92
Alignment explanation
Indices: 2542836--2543376 Score: 976
Period size: 91 Copynumber: 5.9 Consensus size: 92
2542826 GTAATTATTC
2542836 GTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA-TTGTCTTTGTTTT
1 GTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTT
2542900 GTCTTTTGGTTGAAAGTAAATTTGTTCG
66 GTC-TTTGGTTGAAAGTAAATTTGTTCG
2542928 GTTGCTGCCAATTCTGCT-AACTGTGTATTCTTTAACACTGTGAAATA-TATTTGTC-TTGTTTT
1 GTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTT
2542990 GTCTTTTGGTTGAAAGTAAATTTGTTCG
66 GTC-TTTGGTTGAAAGTAAATTTGTTCG
2543018 GCTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTT
1 G-TTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTT
2543082 TGTCTTTTGGTTGAAAGTAAATTTGTTCG
65 TGTC-TTTGGTTGAAAGTAAATTTGTTCG
2543111 GTTGCTG-CAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA-TTGTCTTTGTTTT
1 GTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTT
2543174 GTCTTTGGTTGAAAGTAAATTTGTTCG
66 GTCTTTGGTTGAAAGTAAATTTGTTCG
2543201 GTTGCTGCCAA-TCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTT
1 GTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTT
2543265 GTCTTTGGTTGAAAGTAAATTTGTTCG
66 GTCTTTGGTTGAAAGTAAATTTGTTCG
2543292 GTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AA-AGTATTTGTCTTTGTTTT
1 GTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTT
2543355 GTCTTTGGTTGAAAGTAAATTT
66 GTCTTTGGTTGAAAGTAAATTT
2543377 ATCCATTCAA
Statistics
Matches: 441, Mismatches: 0, Indels: 18
0.96 0.00 0.04
Matches are distributed among these distances:
90 148 0.34
91 163 0.37
92 94 0.21
93 36 0.08
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (92 bp):
GTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTT
GTCTTTGGTTGAAAGTAAATTTGTTCG
Found at i:2543145 original size:183 final size:184
Alignment explanation
Indices: 2542836--2543376 Score: 983
Period size: 183 Copynumber: 3.0 Consensus size: 184
2542826 GTAATTATTC
2542836 GTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA-TTGTCTTTGTTTT
1 GTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTT
2542900 GTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCT-AACTGTGTATTCTTTAAC
66 GTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAAC
2542964 ACTGTGAAATATATTTGTC-TTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCG
131 ACTGTGAAATATATTTGTCTTTGTTTTGTC-TTTGGTTGAAAGTAAATTTGTTCG
2543018 GCTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTT
1 G-TTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTT
2543082 TGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTG-CAATTCTGCTAAACTGTGTATTCTTTAA
65 TGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAA
2543146 CACTGTGAAATAGTA-TTGTCTTTGTTTTGTCTTTGGTTGAAAGTAAATTTGTTCG
130 CACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTGGTTGAAAGTAAATTTGTTCG
2543201 GTTGCTGCCAA-TCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTT
1 GTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTT
2543265 GTC-TTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAAC
66 GTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAAC
*
2543329 ACTGTGAAA-GTATTTGTCTTTGTTTTGTCTTTGGTTGAAAGTAAATTT
131 ACTGTGAAATATATTTGTCTTTGTTTTGTCTTTGGTTGAAAGTAAATTT
2543377 ATCCATTCAA
Statistics
Matches: 350, Mismatches: 1, Indels: 17
0.95 0.00 0.05
Matches are distributed among these distances:
180 2 0.01
181 102 0.29
182 80 0.23
183 154 0.44
184 12 0.03
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (184 bp):
GTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTT
GTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAAC
ACTGTGAAATATATTTGTCTTTGTTTTGTCTTTGGTTGAAAGTAAATTTGTTCG
Found at i:2543445 original size:20 final size:19
Alignment explanation
Indices: 2543420--2543545 Score: 82
Period size: 14 Copynumber: 7.3 Consensus size: 19
2543410 TAGTTTACTT
*
2543420 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-TAAAA
*
2543440 TCGCAACGCGAAAC-CAAA
1 TCGCAACGCGAAACTAAAA
2543458 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACT-AAAA
*
2543477 TCGCAA--CG--AC-AGAA
1 TCGCAACGCGAAACTAAAA
*
2543491 TCGCAACGCG-AAC-CAAA
1 TCGCAACGCGAAACTAAAA
*
2543508 TCGCAA--CG--AC-AAGA
1 TCGCAACGCGAAACTAAAA
*
2543522 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACTAAAA
2543541 TCGCA
1 TCGCA
2543546 TTGCGATTTT
Statistics
Matches: 86, Mismatches: 9, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
14 19 0.22
15 3 0.03
16 4 0.05
17 12 0.14
18 18 0.21
19 17 0.20
20 13 0.15
ACGTcount: A:0.44, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACTAAAA
Found at i:2543512 original size:31 final size:31
Alignment explanation
Indices: 2543454--2543545 Score: 123
Period size: 31 Copynumber: 2.9 Consensus size: 31
2543444 AACGCGAAAC
**
2543454 CAAATCGCAACGCGAAATGAAAATCGCAACGA
1 CAAATCGCAACGCGAAA-CCAAATCGCAACGA
2543486 CAGAATCGCAACGCG-AACCAAATCGCAACGA
1 CA-AATCGCAACGCGAAACCAAATCGCAACGA
2543517 CAAGATCGCAACGCGAAACCAAAATCGCA
1 CAA-ATCGCAACGCGAAACC-AAATCGCA
2543546 TTGCGATTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
30 1 0.02
31 25 0.46
32 8 0.15
33 20 0.37
ACGTcount: A:0.45, C:0.29, G:0.18, T:0.08
Consensus pattern (31 bp):
CAAATCGCAACGCGAAACCAAATCGCAACGA
Found at i:2543543 original size:50 final size:51
Alignment explanation
Indices: 2543420--2543545 Score: 127
Period size: 50 Copynumber: 2.5 Consensus size: 51
2543410 TAGTTTACTT
**
2543420 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAATCGCAACGCGAAA
* * *
2543471 T-G-AAAATCGCAACGACAGAATCGCAACGCG-AACCAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAATCGCAACG-CGAA-A
*
2543522 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
2543546 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
49 3 0.05
50 32 0.53
51 17 0.28
52 6 0.10
53 2 0.03
ACGTcount: A:0.44, C:0.29, G:0.17, T:0.09
Consensus pattern (51 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAATCGCAACGCGAAA
Found at i:2543563 original size:19 final size:19
Alignment explanation
Indices: 2543541--2543674 Score: 110
Period size: 19 Copynumber: 7.6 Consensus size: 19
2543531 GAAACCAAAA
*
2543541 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2543560 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
2543576 T--CGTTGCGATTTTCA-T
1 TCGCGTTGCGATTTTCATT
* *
2543592 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
*
2543608 T--CGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
**
2543625 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
2543644 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
2543664 TCGTGTTGCGA
1 TCGCGTTGCGA
2543675 AAGTAAACTA
Statistics
Matches: 92, Mismatches: 11, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.16
16 14 0.15
17 5 0.05
18 7 0.08
19 39 0.42
20 12 0.13
ACGTcount: A:0.12, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2543582 original size:14 final size:14
Alignment explanation
Indices: 2543563--2543618 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
2543553 TTTCATTTCG
2543563 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
*
2543577 CGTTGCGATTTTCATT
1 CGTTGCGA--TTCTTT
*
2543593 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
2543609 CGTTGCGATT
1 CGTTGCGATT
2543619 TTAATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 16 0.46
16 13 0.37
18 6 0.17
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:2543601 original size:32 final size:33
Alignment explanation
Indices: 2543546--2543637 Score: 150
Period size: 32 Copynumber: 2.8 Consensus size: 33
2543536 CAAAATCGCA
*
2543546 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
2543579 TTGCGATTTTCA-TTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
2543611 TTGCGATTTTAATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
2543638 TTGGTTTCGC
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 29 0.54
33 25 0.46
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:2545652 original size:19 final size:19
Alignment explanation
Indices: 2545636--2545737 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
2545626 AAAAATGACT
2545636 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2545655 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2545674 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2545688 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2545707 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
2545727 ATCGCAATGCG
1 ATCGCAATGCG
2545738 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2545796 original size:19 final size:19
Alignment explanation
Indices: 2545766--2546070 Score: 365
Period size: 19 Copynumber: 17.4 Consensus size: 19
2545756 GATTATCTCG
2545766 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2545784 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2545803 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
2545817 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2545836 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2545855 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2545874 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2545893 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
2545907 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2545926 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2545945 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2545959 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2545978 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2545997 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
2546011 TTGCGATTTTCATTCCGCA
1 TTGCGATTTTCATTTCGCA
2546030 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
2546044 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
2546063 TTGCGATT
1 TTGCGATT
2546071 GTATTTTCCG
Statistics
Matches: 249, Mismatches: 12, Indels: 51
0.80 0.04 0.16
Matches are distributed among these distances:
14 35 0.14
16 31 0.12
17 28 0.11
18 6 0.02
19 149 0.60
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2545850 original size:52 final size:55
Alignment explanation
Indices: 2545744--2546070 Score: 321
Period size: 52 Copynumber: 6.3 Consensus size: 55
2545734 TGCGTTTATA
*
2545744 ATTTCGCATTGCGA-TT-ATCTCG-TTGCGA-TTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTCATTTCGCATTGCGATTTTC
2545795 ATTTCGCATTGCGA-TTC-TTTCG-TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTCATTTCGCATTGCGATTTTC
*
2545847 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGCATTGCGATTTTC
*
2545902 -TGTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGCATTGCGATTTTC
*
2545954 -TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGCATTGCGATTTTC
* * *
2546006 -TCTCG--TTGCGATTTTCATTCCGCATTGCGATTTTCA--T-G--TTGGGATTTTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGCATTGCGATTTTC
*
2546055 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
2546071 GTATTTTCCG
Statistics
Matches: 256, Mismatches: 8, Indels: 24
0.89 0.03 0.08
Matches are distributed among these distances:
47 5 0.02
49 4 0.02
50 5 0.02
51 28 0.11
52 175 0.68
54 7 0.03
55 8 0.03
57 24 0.09
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (55 bp):
ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:2545851 original size:71 final size:71
Alignment explanation
Indices: 2545766--2546004 Score: 364
Period size: 71 Copynumber: 3.4 Consensus size: 71
2545756 GATTATCTCG
2545766 TTGCGA-TTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
2545830 TTCGCA
66 TTCGCA
*
2545836 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG--TTGCGATT
*
2545899 TTC-TGTCG--
61 TTCATTTCGCA
*
2545907 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
2545972 TTCGCA
66 TTCGCA
2545978 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
2546005 CTCTCGTTGC
Statistics
Matches: 153, Mismatches: 5, Indels: 21
0.85 0.03 0.12
Matches are distributed among these distances:
66 6 0.04
68 7 0.05
69 6 0.04
70 6 0.04
71 108 0.71
73 6 0.04
74 8 0.05
76 6 0.04
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (71 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
TTCGCA
Found at i:2549263 original size:20 final size:20
Alignment explanation
Indices: 2549235--2549603 Score: 440
Period size: 20 Copynumber: 18.4 Consensus size: 20
2549225 AAATTTCAGT
* * * *
2549235 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2549255 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
2549275 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2549295 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
*
2549315 GTTGCGATTTACGGTTACGC
1 GTTGCGATTTACGGATACGC
*
2549335 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2549355 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
2549375 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2549395 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2549415 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
2549435 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
2549455 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2549475 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
2549495 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
**
2549515 GTTGCGATTTACGGATACAT
1 GTTGCGATTTACGGATACGC
2549535 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
2549555 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
2549575 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
2549595 GTTGCGATT
1 GTTGCGATT
2549604 ATGGAAAATC
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 5 0.02
20 295 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:2551125 original size:17 final size:18
Alignment explanation
Indices: 2551090--2551128 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
2551080 ATCTTTTGCA
2551090 TTTAATTTATTTAAGTAT
1 TTTAATTTATTTAAGTAT
2551108 TTTAATTTATTTAA-TAT
1 TTTAATTTATTTAAGTAT
2551125 TTTA
1 TTTA
2551129 CTTATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTAATTTATTTAAGTAT
Found at i:2562062 original size:31 final size:31
Alignment explanation
Indices: 2562024--2562093 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
2562014 ACCACAAAAG
*
2562024 AGAAGGAAAGAGAAATCAATGAAATTTAGGA
1 AGAAGGAAAGAGAAAGCAATGAAATTTAGGA
2562055 AGAAGGAAAGAGAAAGCAATGAAATTTAGGA
1 AGAAGGAAAGAGAAAGCAATGAAATTTAGGA
2562086 AGAAGGAA
1 AGAAGGAA
2562094 CCTACACTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.56, C:0.03, G:0.29, T:0.13
Consensus pattern (31 bp):
AGAAGGAAAGAGAAAGCAATGAAATTTAGGA
Found at i:2565577 original size:16 final size:17
Alignment explanation
Indices: 2565556--2565588 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2565546 AAGAAGTTGT
*
2565556 CACCAAC-CTTCAATTC
1 CACCAACGCATCAATTC
2565572 CACCAACGCATCAATTC
1 CACCAACGCATCAATTC
2565589 TCGAATCAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.33, C:0.42, G:0.03, T:0.21
Consensus pattern (17 bp):
CACCAACGCATCAATTC
Found at i:2578589 original size:25 final size:25
Alignment explanation
Indices: 2578561--2578615 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
2578551 TCCCATCATC
2578561 TGCATAAGGTTATGAAGAAAAAGAA
1 TGCATAAGGTTATGAAGAAAAAGAA
2578586 TGCATAAGGTTATGAAGAAAAAGAA
1 TGCATAAGGTTATGAAGAAAAAGAA
2578611 TGCAT
1 TGCAT
2578616 GATAAAACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.49, C:0.05, G:0.24, T:0.22
Consensus pattern (25 bp):
TGCATAAGGTTATGAAGAAAAAGAA
Found at i:2580892 original size:27 final size:25
Alignment explanation
Indices: 2580822--2580898 Score: 79
Period size: 25 Copynumber: 3.0 Consensus size: 25
2580812 TTATATATAC
*
2580822 ATTAACTTGA-TAAATAT-TTTTTTAT
1 ATTAACTT-ATTAAATATATTTTAT-T
2580847 ATTAACTTATTAAATATATTTTATT
1 ATTAACTTATTAAATATATTTTATT
2580872 ATTAACTTAATTTACAA-ATATTTTATT
1 ATTAACTT-A-TTA-AATATATTTTATT
2580899 TTTATTTTCA
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
24 1 0.02
25 24 0.52
26 6 0.13
27 13 0.28
28 2 0.04
ACGTcount: A:0.39, C:0.05, G:0.01, T:0.55
Consensus pattern (25 bp):
ATTAACTTATTAAATATATTTTATT
Found at i:2580919 original size:27 final size:27
Alignment explanation
Indices: 2580841--2580898 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
2580831 ATAAATATTT
2580841 TTTTA-TATTAACTT-A-TTA-AATATA
1 TTTTATTATTAACTTAATTTACAA-ATA
2580865 TTTTATTATTAACTTAATTTACAAATA
1 TTTTATTATTAACTTAATTTACAAATA
2580892 TTTTATT
1 TTTTATT
2580899 TTTATTTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
24 5 0.17
25 9 0.30
26 1 0.03
27 13 0.43
28 2 0.07
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTTATTATTAACTTAATTTACAAATA
Found at i:2583778 original size:19 final size:16
Alignment explanation
Indices: 2583741--2583775 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
2583731 AAATACACCA
2583741 TATTATTTATTTATTT
1 TATTATTTATTTATTT
2583757 TATTATATTATATTATTT
1 TATTAT-TTAT-TTATTT
2583775 T
1 T
2583776 TATAACGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 4 0.24
18 7 0.41
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTATTTATTTATTT
Found at i:2584540 original size:29 final size:26
Alignment explanation
Indices: 2584474--2584532 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
2584464 ATTTTAATAG
2584474 GACAATAATTAACAACAACTATACCC
1 GACAATAATTAACAACAACTATACCC
* *
2584500 GATAATAATTAACAACAACTATGCCC
1 GACAATAATTAACAACAACTATACCC
2584526 GACAATA
1 GACAATA
2584533 GCTATTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.49, C:0.24, G:0.07, T:0.20
Consensus pattern (26 bp):
GACAATAATTAACAACAACTATACCC
Found at i:2589266 original size:179 final size:179
Alignment explanation
Indices: 2588966--2589324 Score: 718
Period size: 179 Copynumber: 2.0 Consensus size: 179
2588956 CTGATGTTAA
2588966 AGATCAGCCTAAGCCACAACCACAGAGCATACTAAAATAAACCAAGAGCTCTGATGCCAATTGTT
1 AGATCAGCCTAAGCCACAACCACAGAGCATACTAAAATAAACCAAGAGCTCTGATGCCAATTGTT
2589031 GTGGAATTCGGGTTAATTTCCACCAATAATAACAAATTCACCTTGAAAACTATTATCTAGGTGAC
66 GTGGAATTCGGGTTAATTTCCACCAATAATAACAAATTCACCTTGAAAACTATTATCTAGGTGAC
2589096 TAGTGTGAAAACTATTGTATTAAAAATCACCCCAAGGTAGATTCCCAAG
131 TAGTGTGAAAACTATTGTATTAAAAATCACCCCAAGGTAGATTCCCAAG
2589145 AGATCAGCCTAAGCCACAACCACAGAGCATACTAAAATAAACCAAGAGCTCTGATGCCAATTGTT
1 AGATCAGCCTAAGCCACAACCACAGAGCATACTAAAATAAACCAAGAGCTCTGATGCCAATTGTT
2589210 GTGGAATTCGGGTTAATTTCCACCAATAATAACAAATTCACCTTGAAAACTATTATCTAGGTGAC
66 GTGGAATTCGGGTTAATTTCCACCAATAATAACAAATTCACCTTGAAAACTATTATCTAGGTGAC
2589275 TAGTGTGAAAACTATTGTATTAAAAATCACCCCAAGGTAGATTCCCAAG
131 TAGTGTGAAAACTATTGTATTAAAAATCACCCCAAGGTAGATTCCCAAG
2589324 A
1 A
2589325 AAGAGTGGAG
Statistics
Matches: 180, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
179 180 1.00
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (179 bp):
AGATCAGCCTAAGCCACAACCACAGAGCATACTAAAATAAACCAAGAGCTCTGATGCCAATTGTT
GTGGAATTCGGGTTAATTTCCACCAATAATAACAAATTCACCTTGAAAACTATTATCTAGGTGAC
TAGTGTGAAAACTATTGTATTAAAAATCACCCCAAGGTAGATTCCCAAG
Found at i:2589561 original size:19 final size:18
Alignment explanation
Indices: 2589533--2589568 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2589523 TTTCACTAAT
*
2589533 AGAGGAAATATTACAAAG
1 AGAGGAAATAGTACAAAG
2589551 AGAGAGAAATAGTACAAA
1 AGAG-GAAATAGTACAAA
2589569 TAGCCTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.58, C:0.06, G:0.22, T:0.14
Consensus pattern (18 bp):
AGAGGAAATAGTACAAAG
Found at i:2591031 original size:32 final size:31
Alignment explanation
Indices: 2590985--2591067 Score: 103
Period size: 32 Copynumber: 2.6 Consensus size: 31
2590975 CCCTAAACCC
* *
2590985 AAACCCAACCCGACCCGAATATCACTCTTAAA
1 AAACCCGA-CCGACCCGAATATCACACTTAAA
* *
2591017 AAACCTGACTCGACCCAAATATCACACTTAAA
1 AAACCCGAC-CGACCCGAATATCACACTTAAA
2591049 AAACCCGACCAGACCCGAA
1 AAACCCGACC-GACCCGAA
2591068 CAAAATAAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
31 2 0.05
32 41 0.95
ACGTcount: A:0.42, C:0.36, G:0.08, T:0.13
Consensus pattern (31 bp):
AAACCCGACCGACCCGAATATCACACTTAAA
Found at i:2591779 original size:26 final size:28
Alignment explanation
Indices: 2591749--2591807 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
2591739 GTTGCTCGAC
*
2591749 TTAAAA-TT-TTGCTCGACTCGTGCTTG
1 TTAAAATTTGTTGCTCGACTCGTGCTCG
2591775 TTAAAAATTTGTTGCTCGACTCGTGCTCG
1 TT-AAAATTTGTTGCTCGACTCGTGCTCG
2591804 TTAA
1 TTAA
2591808 GCTCGATGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 2 0.07
27 4 0.14
28 4 0.14
29 19 0.66
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (28 bp):
TTAAAATTTGTTGCTCGACTCGTGCTCG
Found at i:2595089 original size:20 final size:20
Alignment explanation
Indices: 2595052--2595089 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2595042 TCATTGTTAA
*
2595052 TTTTTTTCTTAATAAATGAT
1 TTTTTTTCTAAATAAATGAT
2595072 TTTTTTTC-AAATATAATG
1 TTTTTTTCTAAATA-AATG
2595090 TGCTTACGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (20 bp):
TTTTTTTCTAAATAAATGAT
Found at i:2595561 original size:2 final size:2
Alignment explanation
Indices: 2595554--2595598 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2595544 AATAAAAATA
2595554 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2595596 AT A
1 AT A
2595599 AGGTTGGGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2596721 original size:21 final size:20
Alignment explanation
Indices: 2596684--2596722 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2596674 AAAATGTCCA
*
2596684 ATAAATATATAATTTAAAAG
1 ATAAATATATAAATTAAAAG
*
2596704 ATAATATATTTAAATTAAA
1 ATAA-ATATATAAATTAAA
2596723 TACAAATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
ATAAATATATAAATTAAAAG
Found at i:2600337 original size:2 final size:2
Alignment explanation
Indices: 2600330--2600357 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2600320 AAAACCGTAA
2600330 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
2600358 CTTGAAGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2606511 original size:2 final size:2
Alignment explanation
Indices: 2606506--2606537 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2606496 GAAAAACTCA
2606506 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2606538 TAAGTTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2606630 original size:47 final size:48
Alignment explanation
Indices: 2606526--2606630 Score: 106
Period size: 47 Copynumber: 2.2 Consensus size: 48
2606516 ATATATATAT
* * * * * * *
2606526 ATATATATATATTAAGTTATTTGTATACAAATTTTATTAAAATTATAT
1 ATATATTTATATTAAGTTATTTGTATAAAAAATATAATAAAATTAGAA
* * *
2606574 AT-TAATTATATTAAGTTGTTTGTGTAAAAAATATAAT-AAATTAGAA
1 ATATATTTATATTAAGTTATTTGTATAAAAAATATAATAAAATTAGAA
2606620 ATATATTTATA
1 ATATATTTATA
2606631 AATATATTTT
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
46 9 0.20
47 34 0.76
48 2 0.04
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.47
Consensus pattern (48 bp):
ATATATTTATATTAAGTTATTTGTATAAAAAATATAATAAAATTAGAA
Found at i:2607870 original size:2 final size:2
Alignment explanation
Indices: 2607863--2607909 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2607853 GAAATTAAAA
2607863 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2607905 AT AT A
1 AT AT A
2607910 GTTATTGGTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2609391 original size:164 final size:164
Alignment explanation
Indices: 2609120--2609444 Score: 587
Period size: 164 Copynumber: 2.0 Consensus size: 164
2609110 AACAGGTAAA
* *
2609120 AATATGATAAAACCGGTGTCATTATGATAAAACCGGTAAACCGCTACCGGATATATTGAAAGTGT
1 AATATGACAAAACCGGTGTCATTATGATAAAACCGGTAAACCGCTACCGAATATATTGAAAGTGT
*
2609185 CGATAAATTAATATAAGTATCGACACTTTTGTAATTTAAAAGAGAAGAAATTATAGCGCCTATAA
66 CGATAAATTAATATAAGTATCGACACTTTTGTAATTTAAAAGAGAAGAAATTATAGCGCCTAAAA
2609250 AGTGTCGATACTTTATACAAATGTATCGATCAAT
131 AGTGTCGATACTTTATACAAATGTATCGATCAAT
*
2609284 AATATGACAAAACCGGTGTCATTATGATAAAACCGGTAAACCTCTACCGAATATATTGAAAGTGT
1 AATATGACAAAACCGGTGTCATTATGATAAAACCGGTAAACCGCTACCGAATATATTGAAAGTGT
* * *
2609349 CGATAAATTAATATAAGTATTGACACTTTTGTAATTTAAAAGAGAAGAAGTTATAGCGCTTAAAA
66 CGATAAATTAATATAAGTATCGACACTTTTGTAATTTAAAAGAGAAGAAATTATAGCGCCTAAAA
2609414 AGTGTCGATACTTTATACAAATGTATCGATC
131 AGTGTCGATACTTTATACAAATGTATCGATC
2609445 CATAGCAATA
Statistics
Matches: 154, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
164 154 1.00
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.30
Consensus pattern (164 bp):
AATATGACAAAACCGGTGTCATTATGATAAAACCGGTAAACCGCTACCGAATATATTGAAAGTGT
CGATAAATTAATATAAGTATCGACACTTTTGTAATTTAAAAGAGAAGAAATTATAGCGCCTAAAA
AGTGTCGATACTTTATACAAATGTATCGATCAAT
Found at i:2609588 original size:182 final size:182
Alignment explanation
Indices: 2609281--2610621 Score: 2149
Period size: 182 Copynumber: 7.4 Consensus size: 182
2609271 TGTATCGATC
* * * *** *
2609281 AATAATATGACAAAACCGGTGTC-ATTATGATAAAACCGGTAAACCTCTACCGAATATATTGAAA
1 AATAATATGACAAAACAGGTCTCGA-AATGATAAAACCGGTAAAAAGCTACCGGATATATTGAAA
* *
2609345 GTGTCGATAAATTAATATAAGTATTGACACTTTTGTAATTTAAAAGAGAAGAAGTTATAGCGCTT
65 GTGTCGATAAATTAATATAAGTATCGACACTTTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCT
2609410 AAAAAGTGTCGATACTTTATACAAATGTATCGATCCATAGCAATATAACAGGT
130 AAAAAGTGTCGATACTTTATACAAATGTATCGATCCATAGCAATATAACAGGT
* *
2609463 AATAATATGACAAAACAGGTCTCGAAATGATAAAACCGGTACAAAGCTACCAGATATATTGAAAG
1 AATAATATGACAAAACAGGTCTCGAAATGATAAAACCGGTAAAAAGCTACCGGATATATTGAAAG
* *
2609528 TGTCGATAAATTAATATAAGTATTGACACTTTTGTAATTTAAAAGAGAAGAAGTTATAGCGCTTA
66 TGTCGATAAATTAATATAAGTATCGACACTTTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTA
*
2609593 AAAAGTGTCGATATTTTATACAAATGTATCGATCCATAGCAATATAACAGGT
131 AAAAGTGTCGATACTTTATACAAATGTATCGATCCATAGCAATATAACAGGT
*
2609645 AATAATATGACAAAACAGGTCTCGAAATGATAAAACCGGTACAAAGCTACCGGATATATTGAAAG
1 AATAATATGACAAAACAGGTCTCGAAATGATAAAACCGGTAAAAAGCTACCGGATATATTGAAAG
2609710 TGTCGATAAATTAATATAAGTATCGACACTTTTG-ATATTT-AAA-AG-AGAAGTTATAGCGCCT
66 TGTCGATAAATTAATATAAGTATCGACACTTTTGTA-ATTTAAAAGAGAAGAAGTTATAGCGCCT
* *
2609771 AAAAAGTGTCAATACTTTATACAAATGTATCGATCCATATCAATATAACAGGT
130 AAAAAGTGTCGATACTTTATACAAATGTATCGATCCATAGCAATATAACAGGT
*
2609824 AATAATATGACAAAACATGTCTCGAAATGATAAAACCGGTAAAAAGCTACCGGATATATTGAAAG
1 AATAATATGACAAAACAGGTCTCGAAATGATAAAACCGGTAAAAAGCTACCGGATATATTGAAAG
2609889 TGTCGATAAATTAATATAAGTATCGACACTTTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTA
66 TGTCGATAAATTAATATAAGTATCGACACTTTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTA
* *
2609954 AAAAGTGTCGATACTTTATACAAATGTATCGATCTATAGCAATATAACATGT
131 AAAAGTGTCGATACTTTATACAAATGTATCGATCCATAGCAATATAACAGGT
* * *
2610006 AATAATATGACAAAACAGGTCTCGAAATGATAAAACTGGTAAAAAGATACCGAATATATTGAAAG
1 AATAATATGACAAAACAGGTCTCGAAATGATAAAACCGGTAAAAAGCTACCGGATATATTGAAAG
* * *
2610071 TATTGAGAAATTAATATAAGTATCGACACTTTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTA
66 TGTCGATAAATTAATATAAGTATCGACACTTTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTA
*
2610136 AAACGTGTCGATACTTTATACAAATGTATCGATCCATAGCAATATAACAGGT
131 AAAAGTGTCGATACTTTATACAAATGTATCGATCCATAGCAATATAACAGGT
2610188 AATAATATGACAAAACAGGTCTCGAAATGATAAAACCGGTAAAAAGCTACCGGATATATTGAAAG
1 AATAATATGACAAAACAGGTCTCGAAATGATAAAACCGGTAAAAAGCTACCGGATATATTGAAAG
* * *
2610253 TGTCGGTAAATTAATATAATTATCGACACTTTT-TATATTTGAAAGAGAAGAAGTTATAGCGCCT
66 TGTCGATAAATTAATATAAGTATCGACACTTTTGTA-ATTTAAAAGAGAAGAAGTTATAGCGCCT
* * *
2610317 AAAAAGTGTCGATATTTTATATAAATGTATCGATCCATAGTAATATAACAGGT
130 AAAAAGTGTCGATACTTTATACAAATGTATCGATCCATAGCAATATAACAGGT
*
2610370 AATAATATGATAAAACAGGTCTCGAAATGATAAAACCGGTAAAAAGCTACCGGATATATTGAAAG
1 AATAATATGACAAAACAGGTCTCGAAATGATAAAACCGGTAAAAAGCTACCGGATATATTGAAAG
* * *
2610435 TGTCGATAAATTAATATAAGTATCGATACTTTCGTAATTTAAAAGAGAAGAAATTATAGCGCCTA
66 TGTCGATAAATTAATATAAGTATCGACACTTTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTA
** *
2610500 AAAAGTGTCGATACTTTATGA-AAATGTATCGATCCATAATAATATAATAGGT
131 AAAAGTGTCGATACTTTAT-ACAAATGTATCGATCCATAGCAATATAACAGGT
* * * * ** * *
2610552 AAAAATATGACAAAACCGGTATCGAAATGACAAAACCGGTAAAGCGCTACC-AATTATGTTGAAA
1 AATAATATGACAAAACAGGTCTCGAAATGATAAAACCGGTAAAAAGCTACCGGA-TATATTGAAA
2610616 GTGTCG
65 GTGTCG
2610622 GTACTTTAAT
Statistics
Matches: 1085, Mismatches: 64, Indels: 20
0.93 0.05 0.02
Matches are distributed among these distances:
179 166 0.15
180 6 0.01
181 9 0.01
182 900 0.83
183 4 0.00
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (182 bp):
AATAATATGACAAAACAGGTCTCGAAATGATAAAACCGGTAAAAAGCTACCGGATATATTGAAAG
TGTCGATAAATTAATATAAGTATCGACACTTTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTA
AAAAGTGTCGATACTTTATACAAATGTATCGATCCATAGCAATATAACAGGT
Found at i:2611206 original size:27 final size:27
Alignment explanation
Indices: 2611175--2611236 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
2611165 TAATAAGAGG
2611175 GATTCAAAATATAATATTTCAACTTCT
1 GATTCAAAATATAATATTTCAACTTCT
2611202 GATTCAAAATATAATATTTCAACTTCT
1 GATTCAAAATATAATATTTCAACTTCT
*
2611229 AATTCAAA
1 GATTCAAA
2611237 TCCAATCTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.39
Consensus pattern (27 bp):
GATTCAAAATATAATATTTCAACTTCT
Found at i:2611960 original size:33 final size:31
Alignment explanation
Indices: 2611918--2612007 Score: 119
Period size: 31 Copynumber: 2.8 Consensus size: 31
2611908 ATAATGTTGT
*
2611918 ACTAAGTGTCCTTACACACTATAGTACCTATGC
1 ACTAAGTGTCCTTATACACTATAGTACC--TGC
* *
2611951 ACTAAGTGTCCTTAATACACCATAGT-GCTGC
1 ACTAAGTGTCCTT-ATACACTATAGTACCTGC
2611982 ACTAAGTGTCCTTATACACTATAGTA
1 ACTAAGTGTCCTTATACACTATAGTA
2612008 TCCTTACATC
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
30 11 0.22
31 16 0.31
33 14 0.27
34 10 0.20
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.31
Consensus pattern (31 bp):
ACTAAGTGTCCTTATACACTATAGTACCTGC
Found at i:2612006 original size:30 final size:30
Alignment explanation
Indices: 2611862--2612006 Score: 130
Period size: 30 Copynumber: 4.7 Consensus size: 30
2611852 ATATGCATTG
* * * *
2611862 AGTGTCCTTACACA-TCACAGTGTTGCATTG
1 AGTGTCCTTACACACT-ATAGTGCTGCACTA
* * * *
2611892 AGCGTCCTTACACACTATAATGTTGTACTA
1 AGTGTCCTTACACACTATAGTGCTGCACTA
*
2611922 AGTGTCCTTACACACTATAGTACCTATGCACTA
1 AGTGTCCTTACACACTATAGT-GC--TGCACTA
* *
2611955 AGTGTCCTTAATACACCATAGTGCTGCACTA
1 AGTGTCCTT-ACACACTATAGTGCTGCACTA
*
2611986 AGTGTCCTTATACACTATAGT
1 AGTGTCCTTACACACTATAGT
2612007 ATCCTTACAT
Statistics
Matches: 95, Mismatches: 15, Indels: 10
0.79 0.12 0.08
Matches are distributed among these distances:
30 52 0.55
31 17 0.18
33 16 0.17
34 10 0.11
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.32
Consensus pattern (30 bp):
AGTGTCCTTACACACTATAGTGCTGCACTA
Found at i:2621262 original size:13 final size:13
Alignment explanation
Indices: 2621244--2621280 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
2621234 ATGTGAGTGC
2621244 ATATGATTATAGT
1 ATATGATTATAGT
2621257 ATATGATTATAGT
1 ATATGATTATAGT
2621270 ATATGATTATA
1 ATATGATTATA
2621281 TGGAAATTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.46
Consensus pattern (13 bp):
ATATGATTATAGT
Found at i:2621769 original size:25 final size:27
Alignment explanation
Indices: 2621728--2621779 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 27
2621718 GCTATGAGCT
*
2621728 TATATGAACATGTGAT-A-TGAAAATG
1 TATATGAACATGAGATAAGTGAAAATG
2621753 TATAGTGAA-ATGAGATAAGTGAAAATG
1 TATA-TGAACATGAGATAAGTGAAAATG
2621780 CCCATGTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 10 0.43
26 5 0.22
27 8 0.35
ACGTcount: A:0.46, C:0.02, G:0.23, T:0.29
Consensus pattern (27 bp):
TATATGAACATGAGATAAGTGAAAATG
Found at i:2621903 original size:21 final size:18
Alignment explanation
Indices: 2621843--2621913 Score: 88
Period size: 18 Copynumber: 3.8 Consensus size: 18
2621833 GGGTCTACGC
* *
2621843 GGTCTTTCGGGATATAGT
1 GGTCCTTCGGGACATAGT
2621861 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
*
2621879 GGTCCTTTGGGACATCTACGT
1 GGTCCTTCGGGACA--TA-GT
2621900 GGTCCTTCGGGACA
1 GGTCCTTCGGGACA
2621914 AATTCTACGT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
18 29 0.63
20 2 0.04
21 15 0.33
ACGTcount: A:0.15, C:0.21, G:0.32, T:0.31
Consensus pattern (18 bp):
GGTCCTTCGGGACATAGT
Found at i:2639721 original size:19 final size:22
Alignment explanation
Indices: 2639697--2639744 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 22
2639687 GACTTATTTA
2639697 ATCATAT-AATC-TAT-ATATC
1 ATCATATAAATCATATAATATC
2639716 ATCATATAAATCATATAATATC
1 ATCATATAAATCATATAATATC
2639738 ATTCATA
1 A-TCATA
2639745 GCACAAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.28
20 4 0.16
21 3 0.12
22 6 0.24
23 5 0.20
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.40
Consensus pattern (22 bp):
ATCATATAAATCATATAATATC
Found at i:2639906 original size:23 final size:23
Alignment explanation
Indices: 2639879--2639938 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
2639869 GCTCGTATAG
*
2639879 ATGCACCGAAGTGCCACGTAGAA
1 ATGCACCGAAGTGCCACATAGAA
* *
2639902 TTGCACC-ATAGTGCCGCATAGAA
1 ATGCACCGA-AGTGCCACATAGAA
*
2639925 ATGCACTGAAGTGC
1 ATGCACCGAAGTGC
2639939 TATATAAGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
22 1 0.03
23 28 0.93
24 1 0.03
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.18
Consensus pattern (23 bp):
ATGCACCGAAGTGCCACATAGAA
Found at i:2641538 original size:20 final size:22
Alignment explanation
Indices: 2641513--2641571 Score: 77
Period size: 20 Copynumber: 2.7 Consensus size: 22
2641503 TTCCCCTTGA
*
2641513 AGTGCATCGATACACTC-T-AC
1 AGTGCATCGATGCACTCTTAAC
*
2641533 AGTGCATCGATGCATTCTTAAC
1 AGTGCATCGATGCACTCTTAAC
2641555 ATGTGCATCGATGCACT
1 A-GTGCATCGATGCACT
2641572 ACCATGTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 15 0.45
21 1 0.03
22 3 0.09
23 14 0.42
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (22 bp):
AGTGCATCGATGCACTCTTAAC
Found at i:2643733 original size:28 final size:29
Alignment explanation
Indices: 2643646--2643851 Score: 305
Period size: 29 Copynumber: 7.1 Consensus size: 29
2643636 ACACAATTAT
*
2643646 CACCCTTTTAAGAAATATTTATAAAACTAA
1 CACCCTTTTAA-AAATATTTACAAAACTAA
*
2643676 CACCCTTTTAAAAATATTTACGAAACTAA
1 CACCCTTTTAAAAATATTTACAAAACTAA
*
2643705 CACCCTTTT-AAAATA-TTACAAAAAATAA
1 CACCCTTTTAAAAATATTTAC-AAAACTAA
2643733 CACCCTTTTAAAAATA-TTACGAAAA-TAA
1 CACCCTTTTAAAAATATTTAC-AAAACTAA
2643761 CACCCTTTTAAAAATATTTACGAAAA-TAA
1 CACCCTTTTAAAAATATTTAC-AAAACTAA
2643790 CACCCTTTTAAAAATATTTACAAAACTAA
1 CACCCTTTTAAAAATATTTACAAAACTAA
*
2643819 CACCCTTTTAAAAATAATTACAAAACTAA
1 CACCCTTTTAAAAATATTTACAAAACTAA
2643848 CACC
1 CACC
2643852 AGGTCAACGG
Statistics
Matches: 166, Mismatches: 6, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
27 4 0.02
28 44 0.27
29 107 0.64
30 11 0.07
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.30
Consensus pattern (29 bp):
CACCCTTTTAAAAATATTTACAAAACTAA
Found at i:2643738 original size:57 final size:58
Alignment explanation
Indices: 2643646--2643851 Score: 310
Period size: 57 Copynumber: 3.6 Consensus size: 58
2643636 ACACAATTAT
* *
2643646 CACCCTTTTAAGAAATATTTATAAAACTAACACCCTTTTAAAAATATTTACGAAACTAA
1 CACCCTTTTAA-AAATATTTACAAAAATAACACCCTTTTAAAAATATTTACGAAACTAA
*
2643705 CACCCTTTT-AAAATA-TTACAAAAAATAACACCCTTTTAAAAATA-TTACGAAAATAA
1 CACCCTTTTAAAAATATTTAC-AAAAATAACACCCTTTTAAAAATATTTACGAAACTAA
* *
2643761 CACCCTTTTAAAAATATTTACGAAAATAACACCCTTTTAAAAATATTTACAAAACTAA
1 CACCCTTTTAAAAATATTTACAAAAATAACACCCTTTTAAAAATATTTACGAAACTAA
* *
2643819 CACCCTTTTAAAAATAATTACAAAACTAACACC
1 CACCCTTTTAAAAATATTTACAAAAATAACACC
2643852 AGGTCAACGG
Statistics
Matches: 134, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
56 23 0.17
57 57 0.43
58 45 0.34
59 9 0.07
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.30
Consensus pattern (58 bp):
CACCCTTTTAAAAATATTTACAAAAATAACACCCTTTTAAAAATATTTACGAAACTAA
Found at i:2643878 original size:13 final size:13
Alignment explanation
Indices: 2643860--2643889 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2643850 CCAGGTCAAC
2643860 GGTCAACGGGTCA
1 GGTCAACGGGTCA
2643873 GGTCAACGGGTCA
1 GGTCAACGGGTCA
2643886 GGTC
1 GGTC
2643890 GAGTCGGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.20, C:0.23, G:0.40, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCA
Found at i:2643905 original size:23 final size:23
Alignment explanation
Indices: 2643873--2643919 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
2643863 CAACGGGTCA
2643873 GGTCAACGGGTCA-GGTCGAGTCG
1 GGTCAACGGGT-AGGGTCGAGTCG
* *
2643896 GGTCAGCGGGTAGGGTCGGGTCG
1 GGTCAACGGGTAGGGTCGAGTCG
2643919 G
1 G
2643920 AACCGGCCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 20 0.95
ACGTcount: A:0.13, C:0.19, G:0.51, T:0.17
Consensus pattern (23 bp):
GGTCAACGGGTAGGGTCGAGTCG
Found at i:2643943 original size:19 final size:20
Alignment explanation
Indices: 2643912--2643955 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
2643902 CGGGTAGGGT
2643912 CGGG-TCGGAACCGGCCAAA
1 CGGGTTCGGAACCGGCCAAA
*
2643931 CGGGTTCGG-ACCGGTCAAA
1 CGGGTTCGGAACCGGCCAAA
*
2643950 CCGGTT
1 CGGGTT
2643956 AAAAATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.20, C:0.30, G:0.36, T:0.14
Consensus pattern (20 bp):
CGGGTTCGGAACCGGCCAAA
Found at i:2644656 original size:29 final size:32
Alignment explanation
Indices: 2644614--2644685 Score: 98
Period size: 29 Copynumber: 2.4 Consensus size: 32
2644604 TTTTGAAAAC
* *
2644614 TTTCATTTAAATCCTCCAATTTCG-C-AAAT-
1 TTTCAATTAAATCCTCAAATTTCGCCAAAATA
2644643 TTTCAATTAAATCCTCAAATTTCGCCAAAATA
1 TTTCAATTAAATCCTCAAATTTCGCCAAAATA
2644675 TTT-AATTAAAT
1 TTTCAATTAAAT
2644686 ATTTTTTCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 22 0.58
30 1 0.03
31 12 0.32
32 3 0.08
ACGTcount: A:0.38, C:0.19, G:0.03, T:0.40
Consensus pattern (32 bp):
TTTCAATTAAATCCTCAAATTTCGCCAAAATA
Found at i:2647877 original size:13 final size:13
Alignment explanation
Indices: 2647859--2647890 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2647849 CCAACACTAT
2647859 GGACTTGCATAAG
1 GGACTTGCATAAG
*
2647872 GGACTTGCCTAAG
1 GGACTTGCATAAG
2647885 GGACTT
1 GGACTT
2647891 TGAACTGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (13 bp):
GGACTTGCATAAG
Found at i:2649469 original size:11 final size:11
Alignment explanation
Indices: 2649453--2649477 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2649443 TAAAATTTAA
2649453 AAACAACTTAT
1 AAACAACTTAT
2649464 AAACAACTTAT
1 AAACAACTTAT
2649475 AAA
1 AAA
2649478 ATTTAAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (11 bp):
AAACAACTTAT
Found at i:2651083 original size:57 final size:58
Alignment explanation
Indices: 2650959--2651090 Score: 171
Period size: 57 Copynumber: 2.3 Consensus size: 58
2650949 ACACAATTAT
*
2650959 CACCCTTTTAAGAAATATTTACAAAACTAACACCATTTTTAAAAAAATTAAGAAAATAA
1 CACCCTTTTAA-AATTATTTACAAAACTAACACCATTTTTAAAAAAATTAAGAAAATAA
* * *
2651018 CACCCTTTTAAAATTATTTATGAAAA-TAACACCA-TTTTAAAAATATTACA-AAACTAA
1 CACCCTTTTAAAATTATTTA-CAAAACTAACACCATTTTTAAAAAAATTA-AGAAAATAA
*
2651075 CACGCTTTTAAAATTA
1 CACCCTTTTAAAATTA
2651091 CAAAACTAAC
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
57 34 0.52
58 17 0.26
59 15 0.23
ACGTcount: A:0.49, C:0.16, G:0.03, T:0.32
Consensus pattern (58 bp):
CACCCTTTTAAAATTATTTACAAAACTAACACCATTTTTAAAAAAATTAAGAAAATAA
Found at i:2651084 original size:28 final size:27
Alignment explanation
Indices: 2650962--2651102 Score: 121
Period size: 29 Copynumber: 5.0 Consensus size: 27
2650952 CAATTATCAC
2650962 CCTTTTAAGAAATATTTACAAAACTAACA
1 CCTTTTAA-AAATA-TTACAAAACTAACA
* *
2650991 CCATTTTTAAAAAAATTA-AGAAAATAACA
1 CC--TTTTAAAAATATTACA-AAACTAACA
* *
2651020 CCCTTTTAAAATTATTTATGAAAA-TAACA
1 -CCTTTTAAAAATA-TTA-CAAAACTAACA
2651049 CCATTTTAAAAATATTACAAAACTAACA
1 CC-TTTTAAAAATATTACAAAACTAACA
2651077 CGCTTTT--AAA-ATTACAAAACTAACA
1 C-CTTTTAAAAATATTACAAAACTAACA
2651102 C
1 C
2651103 ACCGGTCAAC
Statistics
Matches: 96, Mismatches: 6, Indels: 24
0.76 0.05 0.19
Matches are distributed among these distances:
25 16 0.17
26 3 0.03
27 4 0.04
28 25 0.26
29 32 0.33
30 9 0.09
31 7 0.07
ACGTcount: A:0.50, C:0.16, G:0.03, T:0.30
Consensus pattern (27 bp):
CCTTTTAAAAATATTACAAAACTAACA
Found at i:2651129 original size:18 final size:18
Alignment explanation
Indices: 2651106--2651142 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2651096 CTAACACACC
2651106 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
2651124 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
2651142 G
1 G
2651143 AACCGGCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.22, G:0.51, T:0.16
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:2651832 original size:29 final size:29
Alignment explanation
Indices: 2651799--2651859 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
2651789 ATGCTACAAG
2651799 TTTTGAAAACTTT-AATTTAAATCCTCAAA
1 TTTTGAAAACTTTCAA-TTAAATCCTCAAA
* *
2651828 TTTTGCAAATTTTCAATTAAATCCTCAAA
1 TTTTGAAAACTTTCAATTAAATCCTCAAA
2651857 TTT
1 TTT
2651860 CTCCAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 27 0.93
30 2 0.07
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.44
Consensus pattern (29 bp):
TTTTGAAAACTTTCAATTAAATCCTCAAA
Found at i:2653239 original size:42 final size:40
Alignment explanation
Indices: 2653193--2653283 Score: 103
Period size: 40 Copynumber: 2.2 Consensus size: 40
2653183 AGGACTATTG
2653193 CGGCGTTTGAAAAAAAAACGTCACTAAAGTA-GAAGTCTATAA
1 CGGCGTTTGAAAAAAAAAC--CACTAAAGTATG-AGTCTATAA
* * * *
2653235 CGGCGTTTGTATAAAACACCACTAAAGTATGAGTCTATAG
1 CGGCGTTTGAAAAAAAAACCACTAAAGTATGAGTCTATAA
*
2653275 CGACGTTTG
1 CGGCGTTTG
2653284 TAAACAAATG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
40 26 0.60
41 1 0.02
42 16 0.37
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.25
Consensus pattern (40 bp):
CGGCGTTTGAAAAAAAAACCACTAAAGTATGAGTCTATAA
Found at i:2653550 original size:40 final size:39
Alignment explanation
Indices: 2653446--2653533 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 39
2653436 AAAATACATT
* *
2653446 TACTC-ATTGCGGCATTTGTAT-AAAATGCCTCTAAAGTAC
1 TACTCTATTGC-GCGTTT-TATAAAAATGCCGCTAAAGTAC
*
2653485 TACTCTATTGCGCGTTTTAATAAAAATGCCGCTAAATTAC
1 TACTCTATTGCGCGTTTT-ATAAAAATGCCGCTAAAGTAC
2653525 TACTCTATT
1 TACTCTATT
2653534 CGATGTTTGT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
38 1 0.02
39 12 0.28
40 30 0.70
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.36
Consensus pattern (39 bp):
TACTCTATTGCGCGTTTTATAAAAATGCCGCTAAAGTAC
Found at i:2655934 original size:187 final size:187
Alignment explanation
Indices: 2655619--2655993 Score: 750
Period size: 187 Copynumber: 2.0 Consensus size: 187
2655609 CCGAAAAGCT
2655619 TACCATTCACTCTTTGACCAATCCATTGAGGAAGATTTTTCTTCCCACATTAAGGGCTCCGAGTA
1 TACCATTCACTCTTTGACCAATCCATTGAGGAAGATTTTTCTTCCCACATTAAGGGCTCCGAGTA
2655684 CAAGGTTAATCCATCACCCCTACTTCAATATTGAATTCGGAAATTGACCTTTAAACCCAATGTTT
66 CAAGGTTAATCCATCACCCCTACTTCAATATTGAATTCGGAAATTGACCTTTAAACCCAATGTTT
2655749 TTTTTAATTGATTGATGCATGTAATGTATCCGTGATTTGAAGTTCAAAGTTTACAAC
131 TTTTTAATTGATTGATGCATGTAATGTATCCGTGATTTGAAGTTCAAAGTTTACAAC
2655806 TACCATTCACTCTTTGACCAATCCATTGAGGAAGATTTTTCTTCCCACATTAAGGGCTCCGAGTA
1 TACCATTCACTCTTTGACCAATCCATTGAGGAAGATTTTTCTTCCCACATTAAGGGCTCCGAGTA
2655871 CAAGGTTAATCCATCACCCCTACTTCAATATTGAATTCGGAAATTGACCTTTAAACCCAATGTTT
66 CAAGGTTAATCCATCACCCCTACTTCAATATTGAATTCGGAAATTGACCTTTAAACCCAATGTTT
2655936 TTTTTAATTGATTGATGCATGTAATGTATCCGTGATTTGAAGTTCAAAGTTTACAAC
131 TTTTTAATTGATTGATGCATGTAATGTATCCGTGATTTGAAGTTCAAAGTTTACAAC
2655993 T
1 T
2655994 CGTTTTCTCT
Statistics
Matches: 188, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
187 188 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.35
Consensus pattern (187 bp):
TACCATTCACTCTTTGACCAATCCATTGAGGAAGATTTTTCTTCCCACATTAAGGGCTCCGAGTA
CAAGGTTAATCCATCACCCCTACTTCAATATTGAATTCGGAAATTGACCTTTAAACCCAATGTTT
TTTTTAATTGATTGATGCATGTAATGTATCCGTGATTTGAAGTTCAAAGTTTACAAC
Found at i:2661761 original size:8 final size:8
Alignment explanation
Indices: 2661748--2661788 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
2661738 CTCATTTTCA
2661748 GAGAATTT
1 GAGAATTT
2661756 GAGAATTT
1 GAGAATTT
*
2661764 -AGAGTTT
1 GAGAATTT
*
2661771 GGGAATTT
1 GAGAATTT
2661779 GAGAATTT
1 GAGAATTT
2661787 GA
1 GA
2661789 AAGCTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:2662227 original size:127 final size:128
Alignment explanation
Indices: 2661859--2662354 Score: 858
Period size: 128 Copynumber: 3.9 Consensus size: 128
2661849 TAATCGGAGT
* * *
2661859 ACTATTCATATGAAGGCACGTTCCCGGGGGCACGCCTTCCATTATTTTGTCAGAAAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCACGCCTTCCATTATTTTGTCAGAGAATATGTTAT
* *
2661924 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACAGTAGATATATCAGTACCCATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
2661987 ACTATTCACATGAAGGCGCGTTCCCGGGGGCACGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCACGCCTTCCATTATTTTGTCAGAGAATATGTTAT
*
2662052 CATTGCCCTATTATGTCACTCATGTCCCTCGGAGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
** *
2662115 ACTATTCACATGAAGGCGCGTTCCCGGGGGTGCGCCTTCTATTA-TTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCACGCCTTCCATTATTTTGTCAGAGAATATGTTAT
2662179 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
2662242 ACTA-TCACATGAAGGCGCGTTCCCGAGGG--CGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCACGCCTTCCATTATTTTGTCAGAGAATATGTTAT
*
2662304 CATTGCCCTATTATGTCACTCATGTCCCTC-GGGACACTAGATATACCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
2662355 AATCAGGTAA
Statistics
Matches: 354, Mismatches: 13, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
124 31 0.09
125 50 0.14
126 24 0.07
127 86 0.24
128 163 0.46
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCACGCCTTCCATTATTTTGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:2662406 original size:21 final size:21
Alignment explanation
Indices: 2662380--2662423 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
2662370 AACCAAAATT
2662380 AACTTCTTTTGAAAGTTCATC
1 AACTTCTTTTGAAAGTTCATC
2662401 AACTTCTTTTGAAAGTTCATC
1 AACTTCTTTTGAAAGTTCATC
2662422 AA
1 AA
2662424 GTTAAGATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (21 bp):
AACTTCTTTTGAAAGTTCATC
Found at i:2662795 original size:33 final size:34
Alignment explanation
Indices: 2662724--2662820 Score: 142
Period size: 33 Copynumber: 2.9 Consensus size: 34
2662714 ATTTAATGTT
*
2662724 AATTTCGAATACTATAATTTATATTTTAAATTTA
1 AATTTCGAATAATATAATTTATATTTTAAATTTA
* * *
2662758 AATTTCGAATAATATTATTTTTATTTT-TATTTA
1 AATTTCGAATAATATAATTTATATTTTAAATTTA
*
2662791 AATTTCGAATAATATAATTTGTATTTTAAA
1 AATTTCGAATAATATAATTTATATTTTAAA
2662821 AACATTTATC
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 30 0.55
34 25 0.45
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (34 bp):
AATTTCGAATAATATAATTTATATTTTAAATTTA
Found at i:2663441 original size:21 final size:21
Alignment explanation
Indices: 2663332--2663446 Score: 153
Period size: 21 Copynumber: 5.5 Consensus size: 21
2663322 TATGGTATAA
*
2663332 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
2663353 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
2663374 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
2663395 AACCCTGCGGGCTTGGAATGT
1 AACCCTGCGGGCTAGGAATGT
* *
2663416 AACCCTACGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
2663437 AACCCTGCGG
1 AACCCTGCGG
2663447 AGATGGCATA
Statistics
Matches: 87, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
20 3 0.03
21 81 0.93
22 3 0.03
ACGTcount: A:0.21, C:0.26, G:0.34, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:2663476 original size:21 final size:21
Alignment explanation
Indices: 2663450--2663497 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2663440 CCTGCGGAGA
*
2663450 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
2663471 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
2663492 GGGCAT
1 TGGCAT
2663498 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:2666539 original size:88 final size:88
Alignment explanation
Indices: 2666375--2666542 Score: 214
Period size: 88 Copynumber: 1.9 Consensus size: 88
2666365 CTAGAATGAC
* * * * *
2666375 CACAAAAGATGTTAGAGAATGATGATTTTTTACGACGACTAAAAATAGATGAAGAAAATCTTGAT
1 CACAAAAGACGTTAGAAAATGATGATTTTTGACGACGACTAAAAATAGATGAAGAAAATCCTAAT
*
2666440 TCTAATTAAAAAGATGATGAAAT
66 TCTAATGAAAAAGATGATGAAAT
* * *
2666463 CACAAAAGACGTT-GAAAAATGGTGATTTTTGACGACGACTAAAAATATG-TTAAGAAATTCCTA
1 CACAAAAGACGTTAG-AAAATGATGATTTTTGACGACGACTAAAAATA-GATGAAGAAAATCCTA
*
2666526 ATTTTAATGAAAAAGAT
64 ATTCTAATGAAAAAGAT
2666543 TATAGGATGA
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
87 1 0.01
88 66 0.97
89 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.29
Consensus pattern (88 bp):
CACAAAAGACGTTAGAAAATGATGATTTTTGACGACGACTAAAAATAGATGAAGAAAATCCTAAT
TCTAATGAAAAAGATGATGAAAT
Found at i:2667407 original size:20 final size:20
Alignment explanation
Indices: 2667384--2667447 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 20
2667374 TAGTATTTAG
2667384 ATAAAT-TTATTAATAATTTT
1 ATAAATATT-TTAATAATTTT
* *
2667404 AT-AATCTTTTAATAAATTTA
1 ATAAATATTTTAAT-AATTTT
*
2667424 ATAAGTATTTT-ATAATTTT
1 ATAAATATTTTAATAATTTT
*
2667443 TTAAA
1 ATAAA
2667448 CTTTATTGGC
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
19 16 0.46
20 13 0.37
21 6 0.17
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
ATAAATATTTTAATAATTTT
Found at i:2667417 original size:19 final size:20
Alignment explanation
Indices: 2667393--2667442 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
2667383 GATAAATTTA
*
2667393 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
2667412 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
2667433 TT-ATAATTTT
1 TTAATAATTTT
2667443 TTAAACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:2667445 original size:31 final size:30
Alignment explanation
Indices: 2667360--2667446 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
2667350 TTCGATAATA
* *
2667360 TAATAATTATTTTAT-AGTATTTAGATAAATT
1 TAATAA-TATTTTATAATTTTTTA-ATAAATT
* *
2667391 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATTTTTTAATAAATT
2667422 TAATAAGTATTTTATAATTTTTTAA
1 TAATAA-TATTTTATAATTTTTTAA
2667447 ACTTTATTGG
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 40 0.85
32 6 0.13
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (30 bp):
TAATAATATTTTATAATTTTTTAATAAATT
Found at i:2667608 original size:31 final size:31
Alignment explanation
Indices: 2667556--2667616 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
2667546 TTAAACTTAG
* *
2667556 TAAATTTATTAAAAGATTATAAAATTATTAA
1 TAAATTTATTAAAAGACTATAAAATAATTAA
*
2667587 TAAATTTATCT-AAATACTATAAAATAATTA
1 TAAATTTAT-TAAAAGACTATAAAATAATTA
2667617 TTATATTATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (31 bp):
TAAATTTATTAAAAGACTATAAAATAATTAA
Found at i:2667837 original size:17 final size:17
Alignment explanation
Indices: 2667815--2667847 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2667805 ACAGACAGTT
2667815 TATTTCAGTTTATTTTA
1 TATTTCAGTTTATTTTA
2667832 TATTTCAGTTTATTTT
1 TATTTCAGTTTATTTT
2667848 TTCATCTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.67
Consensus pattern (17 bp):
TATTTCAGTTTATTTTA
Found at i:2675767 original size:23 final size:23
Alignment explanation
Indices: 2675734--2675779 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
2675724 GGAATTGGTA
*
2675734 GCAAAATGATGTATTTTGCACCT
1 GCAAAAGGATGTATTTTGCACCT
2675757 GCAAAAGGATGTATTTTGCACCT
1 GCAAAAGGATGTATTTTGCACCT
2675780 TTTTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (23 bp):
GCAAAAGGATGTATTTTGCACCT
Found at i:2683943 original size:20 final size:21
Alignment explanation
Indices: 2683904--2683944 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2683894 CTTGAAATGA
2683904 AATGGTAAACATCAAACAGAT
1 AATGGTAAACATCAAACAGAT
2683925 AATGGTAAACATC-AACAGAT
1 AATGGTAAACATCAAACAGAT
2683945 GTCAAATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.20
Consensus pattern (21 bp):
AATGGTAAACATCAAACAGAT
Found at i:2688378 original size:18 final size:18
Alignment explanation
Indices: 2688355--2688393 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2688345 TTCAATGTAC
2688355 TTAATTATAACA-TTAATT
1 TTAATT-TAACATTTAATT
*
2688373 TTAATTTTACATTTAATT
1 TTAATTTAACATTTAATT
2688391 TTA
1 TTA
2688394 TCACTTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAATTTAACATTTAATT
Found at i:2689948 original size:24 final size:24
Alignment explanation
Indices: 2689913--2689960 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
2689903 GTTTTTAATA
2689913 ATTTTTTCTTTATGACACATTTTT
1 ATTTTTTCTTTATGACACATTTTT
2689937 ATTTTATT-TTTATGACACATTTTT
1 ATTTT-TTCTTTATGACACATTTTT
2689961 CTTAATCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 21 0.91
25 2 0.09
ACGTcount: A:0.23, C:0.10, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTTTTCTTTATGACACATTTTT
Found at i:2689971 original size:24 final size:24
Alignment explanation
Indices: 2689921--2689976 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
2689911 TAATTTTTTC
* *
2689921 TTTATGACACATTTTTATTTTATT
1 TTTATGACACATTTTTACTTAATT
2689945 TTTATGACACATTTTT-CTTAATCT
1 TTTATGACACATTTTTACTTAAT-T
2689969 TTTATGAC
1 TTTATGAC
2689977 GTGTTTTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 4 0.14
24 25 0.86
ACGTcount: A:0.25, C:0.12, G:0.05, T:0.57
Consensus pattern (24 bp):
TTTATGACACATTTTTACTTAATT
Found at i:2690006 original size:23 final size:24
Alignment explanation
Indices: 2689921--2690009 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 24
2689911 TAATTTTTTC
* * *
2689921 TTTATGACACATTTTTATTTTAT-T
1 TTTATGACATATTTTT-CTTAATCT
*
2689945 TTTATGACACATTTTTCTTAATCT
1 TTTATGACATATTTTTCTTAATCT
* *
2689969 TTTATGACGTGTTTTTC-TATATC-
1 TTTATGACATATTTTTCTTA-ATCT
*
2689992 TTTATGATATATTTTTCT
1 TTTATGACATATTTTTCT
2690010 GCCTTTCGAT
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
23 20 0.37
24 34 0.63
ACGTcount: A:0.22, C:0.11, G:0.07, T:0.60
Consensus pattern (24 bp):
TTTATGACATATTTTTCTTAATCT
Found at i:2691297 original size:50 final size:50
Alignment explanation
Indices: 2691239--2691336 Score: 196
Period size: 50 Copynumber: 2.0 Consensus size: 50
2691229 AAGTTCAAAT
2691239 AGGTAAGTAAAAGATGAAAAAGATGCTCAAATCAAGTGATATCTGTGAAA
1 AGGTAAGTAAAAGATGAAAAAGATGCTCAAATCAAGTGATATCTGTGAAA
2691289 AGGTAAGTAAAAGATGAAAAAGATGCTCAAATCAAGTGATATCTGTGA
1 AGGTAAGTAAAAGATGAAAAAGATGCTCAAATCAAGTGATATCTGTGA
2691337 TAAAAGAATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.47, C:0.08, G:0.22, T:0.22
Consensus pattern (50 bp):
AGGTAAGTAAAAGATGAAAAAGATGCTCAAATCAAGTGATATCTGTGAAA
Found at i:2697290 original size:17 final size:18
Alignment explanation
Indices: 2697262--2697295 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2697252 AAAATCGTTG
2697262 ATCTGCGGATAATTAATT
1 ATCTGCGGATAATTAATT
2697280 ATCTG-GGATAATTAAT
1 ATCTGCGGATAATTAAT
2697296 ATATACTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (18 bp):
ATCTGCGGATAATTAATT
Found at i:2707585 original size:486 final size:486
Alignment explanation
Indices: 2706668--2708135 Score: 2810
Period size: 486 Copynumber: 3.0 Consensus size: 486
2706658 TTTCGTCCCC
* * *
2706668 TAGAACTTTATAAGTTCAAGTACATCCCTTTGAAATTTTATAAGTTTAAATTCGTCTCCCAACAT
1 TAGAATTTTATAAGTTCAAATACATCCCTTTGAAATTTTATAAGTTTAAGTTCGTCTCCCAACAT
* * *
2706733 AAAATCCTGTACCTGTCCTTAGTGATGACTATCGTTCGAGGTCAGTAGGTTTGTGTACCCGGGTA
66 AAAATCCTGTACATATCCTTAGTGATGACTATCATTCGAGGTCAGTAGGTTTGTGTACCCGGGTA
*
2706798 TGGGACAACAACCGTTTTGGTAAGGGTGACCTGAATCGTTGCTGCTTTACTTATGTATTAGATTA
131 TGGGACAACAACCGTTTTGGTAAGGGTGACCTGAATCGTTGCTGCTTTACTTGTGTATTAGATTA
*
2706863 AATGTGTGGGATTAGTATCTCCTTCTTGTGCACTCTTGTCATTGATATGTACATTCTTTTTCTTT
196 AATGTGTGGGATTAGTATCTCCTTCTTGTGCACTCTTGTCATTGATATGTACATTCTTTTTCTAT
2706928 CATTTAAGTTTAGGGAGGCTTTTTTAACAAGCTCACATCTATATCTTATTTTGTGCGACCCTTTT
261 CATTTAAGTTTAGGGAGGCTTTTTTAACAAGCTCACATCTATATCTTATTTTGTGCGACCCTTTT
2706993 ATAACATACAAAATATACCCTTTACAAAAAGAAAGATTTTATAAATTCCAGTTTCTTTTTATAAT
326 ATAACATACAAAATATACCCTTTACAAAAAGAAAGATTTTATAAATTCCAGTTTCTTTTTATAAT
2707058 TTGTTATGGATTTCTATAGAGTGTTTGTGAAGATAAATTGTTAGTGAATATATCCAATTTGTTTA
391 TTGTTATGGATTTCTATAGAGTGTTTGTGAAGATAAATTGTTAGTGAATATATCCAATTTGTTTA
2707123 TATGCTCTAATAATAGATTCTTAGTTTATAG
456 TATGCTCTAATAATAGATTCTTAGTTTATAG
2707154 TAGAATTTTATAAGTTCAAATACATCCCTTTGAAATTTTATAAGTTTAAGTTCGTCTCCCAACAT
1 TAGAATTTTATAAGTTCAAATACATCCCTTTGAAATTTTATAAGTTTAAGTTCGTCTCCCAACAT
2707219 AAAATCCTGTACATATCCTTAGTGATGACTATCATTCGAGGTCAGTAGGTTTGTGTACCCGGGTA
66 AAAATCCTGTACATATCCTTAGTGATGACTATCATTCGAGGTCAGTAGGTTTGTGTACCCGGGTA
2707284 TGGGACAACAACCGTTTTGGTAAGGGTGACCTGAATCGTTGCTGCTTTACTTGTGTATTAGATTA
131 TGGGACAACAACCGTTTTGGTAAGGGTGACCTGAATCGTTGCTGCTTTACTTGTGTATTAGATTA
2707349 AATGTGTGGGATTAGTATCTCCTTCTTGTGCACTCTTGTCATTGATATGTACATTCTTTTTCTAT
196 AATGTGTGGGATTAGTATCTCCTTCTTGTGCACTCTTGTCATTGATATGTACATTCTTTTTCTAT
2707414 CATTTAAGTTTAGGGAGGCTTTTTTAACAAGCTCACATCTATATCTTATTTTGTGCGACCCTTTT
261 CATTTAAGTTTAGGGAGGCTTTTTTAACAAGCTCACATCTATATCTTATTTTGTGCGACCCTTTT
2707479 ATAACATACAAAATATACCCTTTACAAAAAGAAAGATTTTATAAATTCCAGTTTCTTTTTATAAT
326 ATAACATACAAAATATACCCTTTACAAAAAGAAAGATTTTATAAATTCCAGTTTCTTTTTATAAT
2707544 TTGTTATGGATTTCTATAGAGTGTTTGTGAAGATAAATTGTTAGTGAATATATCCAATTTGTTTA
391 TTGTTATGGATTTCTATAGAGTGTTTGTGAAGATAAATTGTTAGTGAATATATCCAATTTGTTTA
2707609 TATGCTCTAATAATAGATTCTTAGTTTATAG
456 TATGCTCTAATAATAGATTCTTAGTTTATAG
2707640 TAGAATTTTATAAGTTCAAATACATCCCTTTGAAATTTTATAAGTTTAAGTTCGTCTCCCAACAT
1 TAGAATTTTATAAGTTCAAATACATCCCTTTGAAATTTTATAAGTTTAAGTTCGTCTCCCAACAT
2707705 AAAATCCTGTACATATCCTTAGTGATGACTATCATTCGAGGTCAGTAGGTTTGTGTACCCGGGTA
66 AAAATCCTGTACATATCCTTAGTGATGACTATCATTCGAGGTCAGTAGGTTTGTGTACCCGGGTA
2707770 TGGGACAACAACCGTTTTGGTAAGGGTGACCTGAATCGTTGCTGCTTTACTTGTGTATTAGATTA
131 TGGGACAACAACCGTTTTGGTAAGGGTGACCTGAATCGTTGCTGCTTTACTTGTGTATTAGATTA
2707835 AATGTGTGGGATTAGTATCTCCTTCTTGTGCACTCTTGTCATTGATATGTACATTCTTTTTCTAT
196 AATGTGTGGGATTAGTATCTCCTTCTTGTGCACTCTTGTCATTGATATGTACATTCTTTTTCTAT
2707900 CATTTAAGTTTAGGGAGGCTTTTTTAACAAGCTCACATCTATATCTTATTTTGTGCGTGTCACCC
261 CATTTAAGTTTAGGGAGGCTTTTTTAACAAGCTCACATCTATATCTTATTTTGTGC--G--ACCC
*
2707965 TTTTATAACATACAAAATATACCCTTTACAAAAGGAAAGATTTTATAAATTCCAGTTTCTTTTTA
322 TTTTATAACATACAAAATATACCCTTTACAAAAAGAAAGATTTTATAAATTCCAGTTTCTTTTTA
*
2708030 TAATTTGTTATGGATTTCTATAGAATGTTTGTGAAGATAAATTGTTAGTGAATATATCCAATTTG
387 TAATTTGTTATGGATTTCTATAGAGTGTTTGTGAAGATAAATTGTTAGTGAATATATCCAATTTG
2708095 TTTATATGCTCTAATAATAGATTCTTAGTTTATAG
452 TTTATATGCTCTAATAATAGATTCTTAGTTTATAG
2708130 TAGAAT
1 TAGAAT
2708136 AACTTAAATT
Statistics
Matches: 968, Mismatches: 10, Indels: 4
0.99 0.01 0.00
Matches are distributed among these distances:
486 794 0.82
488 1 0.00
490 173 0.18
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (486 bp):
TAGAATTTTATAAGTTCAAATACATCCCTTTGAAATTTTATAAGTTTAAGTTCGTCTCCCAACAT
AAAATCCTGTACATATCCTTAGTGATGACTATCATTCGAGGTCAGTAGGTTTGTGTACCCGGGTA
TGGGACAACAACCGTTTTGGTAAGGGTGACCTGAATCGTTGCTGCTTTACTTGTGTATTAGATTA
AATGTGTGGGATTAGTATCTCCTTCTTGTGCACTCTTGTCATTGATATGTACATTCTTTTTCTAT
CATTTAAGTTTAGGGAGGCTTTTTTAACAAGCTCACATCTATATCTTATTTTGTGCGACCCTTTT
ATAACATACAAAATATACCCTTTACAAAAAGAAAGATTTTATAAATTCCAGTTTCTTTTTATAAT
TTGTTATGGATTTCTATAGAGTGTTTGTGAAGATAAATTGTTAGTGAATATATCCAATTTGTTTA
TATGCTCTAATAATAGATTCTTAGTTTATAG
Found at i:2709345 original size:21 final size:21
Alignment explanation
Indices: 2709320--2709366 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
2709310 TCCTGCCCTG
2709320 GTATCGATACTCTATGAATGA
1 GTATCGATACTCTATGAATGA
2709341 GTATCGATACTCTATGAATGA
1 GTATCGATACTCTATGAATGA
2709362 GTATC
1 GTATC
2709367 AATATTAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (21 bp):
GTATCGATACTCTATGAATGA
Found at i:2715537 original size:21 final size:21
Alignment explanation
Indices: 2715511--2715551 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2715501 CCGATAATCG
**
2715511 AGCATGAATACGGTAAGGAAT
1 AGCATGAATACAATAAGGAAT
2715532 AGCATGAATACAATAAGGAA
1 AGCATGAATACAATAAGGAA
2715552 GAACACCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.10, G:0.24, T:0.17
Consensus pattern (21 bp):
AGCATGAATACAATAAGGAAT
Found at i:2717593 original size:17 final size:17
Alignment explanation
Indices: 2717552--2717593 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
2717542 GATTATCCCT
*
2717552 CAAAAAAACATTGTAGG
1 CAAAAAAACATTGTACG
*
2717569 CAAGAAAACCATTGTACG
1 CAA-AAAAACATTGTACG
2717587 CAAAAAA
1 CAAAAAA
2717594 TAAAGTACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.55, C:0.17, G:0.14, T:0.14
Consensus pattern (17 bp):
CAAAAAAACATTGTACG
Found at i:2718162 original size:47 final size:47
Alignment explanation
Indices: 2718097--2718188 Score: 148
Period size: 47 Copynumber: 2.0 Consensus size: 47
2718087 AGTTGAGCTG
* * *
2718097 GGTAGTTGGTGAGATTTATGACTGTCCGATTGAAATAATTGAAGGTA
1 GGTAGATGGTGAGATTTATGACCGTCCGATTAAAATAATTGAAGGTA
*
2718144 GGTAGATGGTGAGGTTTATGACCGTCCGATTAAAATAATTGAAGG
1 GGTAGATGGTGAGATTTATGACCGTCCGATTAAAATAATTGAAGG
2718189 GGTGGCAGGA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.30, C:0.08, G:0.30, T:0.32
Consensus pattern (47 bp):
GGTAGATGGTGAGATTTATGACCGTCCGATTAAAATAATTGAAGGTA
Found at i:2719778 original size:13 final size:13
Alignment explanation
Indices: 2719760--2719784 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2719750 GTTGGAAAGG
2719760 GATGAATTTAATT
1 GATGAATTTAATT
2719773 GATGAATTTAAT
1 GATGAATTTAAT
2719785 ATTTATATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (13 bp):
GATGAATTTAATT
Found at i:2720226 original size:34 final size:34
Alignment explanation
Indices: 2720187--2720253 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
2720177 AAAAGGAGTT
*
2720187 TTATCTCTTGAATATTTCA-AATTAAAAGATATTG
1 TTATCTATTGAATA-TTCACAATTAAAAGATATTG
* * *
2720221 TTATCTATTTAATATTGACTATTAAAAGATATT
1 TTATCTATTGAATATTCACAATTAAAAGATATT
2720254 TGGTTGGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 3 0.11
34 25 0.89
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (34 bp):
TTATCTATTGAATATTCACAATTAAAAGATATTG
Found at i:2720372 original size:20 final size:20
Alignment explanation
Indices: 2720347--2720396 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
2720337 GTTCTAGAAG
2720347 TTTTCTTCTCTT-GAAAAATA
1 TTTTCTTCTCTTAG-AAAATA
2720367 TTTTC-TCTCCTTAGAAAATA
1 TTTTCTTCT-CTTAGAAAATA
2720387 --TTCTTCTCTT
1 TTTTCTTCTCTT
2720397 CCACTAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
18 6 0.22
19 6 0.22
20 14 0.52
21 1 0.04
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.52
Consensus pattern (20 bp):
TTTTCTTCTCTTAGAAAATA
Found at i:2723878 original size:15 final size:16
Alignment explanation
Indices: 2723841--2723878 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2723831 CATACCAATT
*
2723841 TTGTTTGTCTTAAAAA
1 TTGTTTTTCTTAAAAA
*
2723857 TTATTTTTCTT-AAAA
1 TTGTTTTTCTTAAAAA
2723872 TTGTTTT
1 TTGTTTT
2723879 AAAGCGTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.26, C:0.05, G:0.08, T:0.61
Consensus pattern (16 bp):
TTGTTTTTCTTAAAAA
Found at i:2724280 original size:174 final size:174
Alignment explanation
Indices: 2723990--2724340 Score: 702
Period size: 174 Copynumber: 2.0 Consensus size: 174
2723980 AGCAATAATT
2723990 TAGGGTTTTCATCGAAAACCTATTCGTTTCATAAAAAAGACGTTACGACAGATAACAAAAGTAAT
1 TAGGGTTTTCATCGAAAACCTATTCGTTTCATAAAAAAGACGTTACGACAGATAACAAAAGTAAT
2724055 GTTATGTGTATTTGTTGAAAGAGCTAAACGAAGTTATAGAAACAATTATTTTCTATAAACATGAA
66 GTTATGTGTATTTGTTGAAAGAGCTAAACGAAGTTATAGAAACAATTATTTTCTATAAACATGAA
2724120 GTTGAAAATCAACTTAATAAATAAATTAAGATGGTAAGAAGTGA
131 GTTGAAAATCAACTTAATAAATAAATTAAGATGGTAAGAAGTGA
2724164 TAGGGTTTTCATCGAAAACCTATTCGTTTCATAAAAAAGACGTTACGACAGATAACAAAAGTAAT
1 TAGGGTTTTCATCGAAAACCTATTCGTTTCATAAAAAAGACGTTACGACAGATAACAAAAGTAAT
2724229 GTTATGTGTATTTGTTGAAAGAGCTAAACGAAGTTATAGAAACAATTATTTTCTATAAACATGAA
66 GTTATGTGTATTTGTTGAAAGAGCTAAACGAAGTTATAGAAACAATTATTTTCTATAAACATGAA
2724294 GTTGAAAATCAACTTAATAAATAAATTAAGATGGTAAGAAGTGA
131 GTTGAAAATCAACTTAATAAATAAATTAAGATGGTAAGAAGTGA
2724338 TAG
1 TAG
2724341 TGATGGTGAA
Statistics
Matches: 177, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
174 177 1.00
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (174 bp):
TAGGGTTTTCATCGAAAACCTATTCGTTTCATAAAAAAGACGTTACGACAGATAACAAAAGTAAT
GTTATGTGTATTTGTTGAAAGAGCTAAACGAAGTTATAGAAACAATTATTTTCTATAAACATGAA
GTTGAAAATCAACTTAATAAATAAATTAAGATGGTAAGAAGTGA
Found at i:2727696 original size:17 final size:18
Alignment explanation
Indices: 2727659--2727697 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
2727649 ATTATTTCTC
*
2727659 TCTTGTTTCTCTATTGAT
1 TCTTCTTTCTCTATTGAT
*
2727677 TCTTCTTTCT-TATTGTT
1 TCTTCTTTCTCTATTGAT
2727694 TCTT
1 TCTT
2727698 GTTGTTGATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.08, C:0.18, G:0.08, T:0.67
Consensus pattern (18 bp):
TCTTCTTTCTCTATTGAT
Found at i:2727992 original size:26 final size:26
Alignment explanation
Indices: 2727963--2728012 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
2727953 AAAATAGCCA
*
2727963 GAGTGCATCGATGCATCAAATGCACT
1 GAGTGCATCGATGCATAAAATGCACT
2727989 GAGTGCATCGATGCATAAAATGCA
1 GAGTGCATCGATGCATAAAATGCA
2728013 TTCGATGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (26 bp):
GAGTGCATCGATGCATAAAATGCACT
Found at i:2732859 original size:20 final size:20
Alignment explanation
Indices: 2732817--2732859 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
2732807 TTATTTTCAT
*
2732817 TTTTTAATTTTAAAATATCA
1 TTTTTAATTTTAAAATATAA
2732837 TTTTTATATTTTAAAA-ATAA
1 TTTTTA-ATTTTAAAATATAA
2732857 TTT
1 TTT
2732860 CTCATAATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTTAATTTTAAAATATAA
Done.