Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold230
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: 2055625
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 11 of 14
Found at i:1259324 original size:38 final size:37
Alignment explanation
Indices: 1259282--1259364 Score: 89
Period size: 38 Copynumber: 2.2 Consensus size: 37
1259272 ATATGAATAA
*
1259282 ATTAATTAA-AAATAATTTAAAT-TTATATAATATAAATT
1 ATTAATTAATAAA-AATTTAAATAATATATAAT-T-AATT
* *
1259320 ATTAATATAATAAAATTTTATATAATATATAATTAATT
1 ATTAAT-TAATAAAAATTTAAATAATATATAATTAATT
1259358 ATTAATT
1 ATTAATT
1259365 GCTTTTTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
37 1 0.03
38 16 0.41
39 11 0.28
40 11 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (37 bp):
ATTAATTAATAAAAATTTAAATAATATATAATTAATT
Found at i:1259327 original size:18 final size:17
Alignment explanation
Indices: 1259304--1259363 Score: 72
Period size: 18 Copynumber: 3.5 Consensus size: 17
1259294 TAATTTAAAT
1259304 TTATATAATATAAATTA
1 TTATATAATATAAATTA
1259321 TTAATATAATA-AAATT-
1 TT-ATATAATATAAATTA
1259337 TTATATAATATATAATTAA
1 TTATATAATATA-AATT-A
1259356 TTAT-TAAT
1 TTATATAAT
1259364 TGCTTTTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
15 8 0.21
16 3 0.08
17 11 0.29
18 12 0.32
19 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTATATAATATAAATTA
Found at i:1259344 original size:15 final size:16
Alignment explanation
Indices: 1259293--1259353 Score: 72
Period size: 15 Copynumber: 3.8 Consensus size: 16
1259283 TTAATTAAAA
*
1259293 ATAATTTAAA-TTTAT
1 ATAATATAAATTTTAT
1259308 ATAATATAAATTATTAAT
1 ATAATATAAATT-TT-AT
1259326 ATAATA-AAATTTTAT
1 ATAATATAAATTTTAT
1259341 ATAATATATAATT
1 ATAATATA-AATT
1259354 AATTATTAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
15 17 0.43
16 4 0.10
17 11 0.28
18 8 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAATATAAATTTTAT
Found at i:1262132 original size:47 final size:47
Alignment explanation
Indices: 1262064--1262153 Score: 119
Period size: 47 Copynumber: 1.9 Consensus size: 47
1262054 ATTGAATATA
* ** *
1262064 ATAATATTATTATAAATAATATATTAATTAATTTTAAAAATTATTTT
1 ATAATATTATGATAAATAATATAAAAATAAATTTTAAAAATTATTTT
*
1262111 ATAATATTATGATATAA-AATATAAAAATAAATTTTAAATATTA
1 ATAATATTATGATA-AATAATATAAAAATAAATTTTAAAAATTA
1262154 AATTTTAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
47 35 0.95
48 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (47 bp):
ATAATATTATGATAAATAATATAAAAATAAATTTTAAAAATTATTTT
Found at i:1262157 original size:14 final size:14
Alignment explanation
Indices: 1262138--1262183 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
1262128 AATATAAAAA
1262138 TAAATTTTAAATAT
1 TAAATTTTAAATAT
1262152 TAAATTTTAAAT-T
1 TAAATTTTAAATAT
*
1262165 ATAAATTATAAATA-
1 -TAAATTTTAAATAT
1262179 TAAAT
1 TAAAT
1262184 AAAAAATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 6 0.21
14 23 0.79
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TAAATTTTAAATAT
Found at i:1262168 original size:41 final size:41
Alignment explanation
Indices: 1262123--1262205 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 41
1262113 AATATTATGA
***
1262123 TATAAAATATAAAAATAAATTTTAAATATTAAATTTTA-AAT
1 TATAAAATATAAAAATAAATAAAAAAT-TTAAATTTTATAAT
* *
1262164 TATAAATTATAAATATAAATAAAAAATTTAAATTTTATAAT
1 TATAAAATATAAAAATAAATAAAAAATTTAAATTTTATAAT
1262205 T
1 T
1262206 TTTAAAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
40 10 0.28
41 26 0.72
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (41 bp):
TATAAAATATAAAAATAAATAAAAAATTTAAATTTTATAAT
Found at i:1262207 original size:8 final size:7
Alignment explanation
Indices: 1262138--1262207 Score: 54
Period size: 7 Copynumber: 10.1 Consensus size: 7
1262128 AATATAAAAA
1262138 TAAATTT
1 TAAATTT
*
1262145 TAAATAT
1 TAAATTT
1262152 TAAATTT
1 TAAATTT
*
1262159 TAAATTA
1 TAAATTT
*
1262166 TAAATTA
1 TAAATTT
*
1262173 TAAA-TA
1 TAAATTT
*
1262179 TAAA-TA
1 TAAATTT
* *
1262185 AAAAATT
1 TAAATTT
1262192 TAAATTT
1 TAAATTT
1262199 TATAATTT
1 TA-AATTT
1262207 T
1 T
1262208 TAAAAAATTA
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
6 11 0.20
7 37 0.69
8 6 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
TAAATTT
Found at i:1265132 original size:2 final size:2
Alignment explanation
Indices: 1265125--1265152 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1265115 GAGGGGACAT
1265125 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1265153 TGGAAGTCTC
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1266528 original size:11 final size:12
Alignment explanation
Indices: 1266512--1266543 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1266502 TTGTTAATCG
1266512 ATTATATATAT-
1 ATTATATATATA
1266523 ATTATATA-ATA
1 ATTATATATATA
1266534 ATTATATATA
1 ATTATATATA
1266544 CTTTTAGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 2 0.11
11 16 0.84
12 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTATATATATA
Found at i:1273230 original size:18 final size:17
Alignment explanation
Indices: 1273207--1273244 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1273197 AGCAACTAAT
1273207 ATATTAT-TTATAATAGTA
1 ATATTATATTA-AAT-GTA
1273225 ATATTATATTAAATGTA
1 ATATTATATTAAATGTA
1273242 ATA
1 ATA
1273245 ATTGATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 10 0.53
19 3 0.16
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (17 bp):
ATATTATATTAAATGTA
Found at i:1275900 original size:3 final size:3
Alignment explanation
Indices: 1275849--1275884 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1275839 TGAACAAAGA
1275849 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1275885 AAGCATGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1277219 original size:17 final size:18
Alignment explanation
Indices: 1277179--1277219 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
1277169 ATTATTAAAT
1277179 ATATAAATATTAATATAA
1 ATATAAATATTAATATAA
*
1277197 AAATAACAT-TTAA-ATAA
1 ATATAA-ATATTAATATAA
1277214 ATATAA
1 ATATAA
1277220 TAAATAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 9 0.45
18 9 0.45
19 2 0.10
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (18 bp):
ATATAAATATTAATATAA
Found at i:1277765 original size:21 final size:23
Alignment explanation
Indices: 1277737--1277786 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
1277727 AATTAAATTA
*
1277737 TAATTTAAAATTTTA-TTATTTT
1 TAATTTAAAATTTAATTTATTTT
1277759 T-ATTT-AAATTTAATTTATTTT
1 TAATTTAAAATTTAATTTATTTT
1277780 TAATTTA
1 TAATTTA
1277787 TTTAATTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 7 0.29
21 12 0.50
22 5 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TAATTTAAAATTTAATTTATTTT
Found at i:1277781 original size:11 final size:11
Alignment explanation
Indices: 1277752--1277789 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1277742 TAAAATTTTA
1277752 TTATTTTT-AT
1 TTATTTTTAAT
**
1277762 TTAAATTTAAT
1 TTATTTTTAAT
1277773 TTATTTTTAAT
1 TTATTTTTAAT
1277784 TTATTT
1 TTATTT
1277790 AATTTGTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
10 6 0.26
11 17 0.74
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTTTTAAT
Found at i:1277851 original size:16 final size:16
Alignment explanation
Indices: 1277752--1277854 Score: 59
Period size: 17 Copynumber: 6.2 Consensus size: 16
1277742 TAAAATTTTA
*
1277752 TTATTT-TTATTTAAAT
1 TTATTTATT-TTTATAT
1277768 TTAATTTATTTTTA-AT
1 TT-ATTTATTTTTATAT
*
1277784 TTATTTAATTTGTATAT
1 TTATTT-ATTTTTATAT
*
1277801 TTATTTTATTATTT-TAAA
1 TTA-TTTATT-TTTAT-AT
* * * *
1277819 ATATTAAAATATTATAT
1 TTATT-TATTTTTATAT
1277836 TTATTTATTTTTATAT
1 TTATTTATTTTTATAT
1277852 TTA
1 TTA
1277855 AATTTTAAAT
Statistics
Matches: 66, Mismatches: 12, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
15 4 0.06
16 23 0.35
17 26 0.39
18 13 0.20
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (16 bp):
TTATTTATTTTTATAT
Found at i:1277872 original size:21 final size:21
Alignment explanation
Indices: 1277848--1277902 Score: 58
Period size: 23 Copynumber: 2.6 Consensus size: 21
1277838 ATTTATTTTT
*
1277848 ATATTTAAATTTTAAATAAAA
1 ATATTTAAATTATAAATAAAA
* *
1277869 ATATTTTAAAATAATAAATAAAT
1 ATA-TTT-AAATTATAAATAAAA
1277892 A-ATTTAAATTA
1 ATATTTAAATTA
1277903 AATTAAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 5 0.18
21 6 0.21
22 4 0.14
23 13 0.46
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATTTAAATTATAAATAAAA
Found at i:1277876 original size:15 final size:17
Alignment explanation
Indices: 1277856--1277888 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1277846 TTATATTTAA
1277856 ATTTT-AAATAA-AAAT
1 ATTTTAAAATAATAAAT
1277871 ATTTTAAAATAATAAAT
1 ATTTTAAAATAATAAAT
1277888 A
1 A
1277889 AATAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 6 0.38
17 5 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATTTTAAAATAATAAAT
Found at i:1278428 original size:2 final size:2
Alignment explanation
Indices: 1278421--1278450 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1278411 CAAGGGCAGA
1278421 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
1278451 TAAAAAGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1278569 original size:18 final size:19
Alignment explanation
Indices: 1278536--1278571 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1278526 ATTTTCACAT
1278536 ATTTAATAATATATATTAA
1 ATTTAATAATATATATTAA
*
1278555 ATTTATTAA-ATATATTA
1 ATTTAATAATATATATTA
1278572 TTTTTATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTAATAATATATATTAA
Found at i:1281304 original size:15 final size:16
Alignment explanation
Indices: 1281280--1281314 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1281270 TGTAATTTTT
*
1281280 AATTATATTAA-AAAA
1 AATTAAATTAATAAAA
1281295 AATTAAATTAATAAAA
1 AATTAAATTAATAAAA
1281311 AATT
1 AATT
1281315 GATTATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AATTAAATTAATAAAA
Found at i:1281400 original size:22 final size:22
Alignment explanation
Indices: 1281372--1281415 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1281362 TCATGTAAAA
*
1281372 ATATTTTTGATGAAAATTAGGT
1 ATATTTTCGATGAAAATTAGGT
* *
1281394 ATATTTTCGGTGGAAATTAGGT
1 ATATTTTCGATGAAAATTAGGT
1281416 TGAAAAAATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.23, T:0.43
Consensus pattern (22 bp):
ATATTTTCGATGAAAATTAGGT
Found at i:1283379 original size:18 final size:18
Alignment explanation
Indices: 1283352--1283387 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1283342 TATAAATATA
1283352 TTTAATATTTTTA-AATT
1 TTTAATATTTTTATAATT
1283369 TTTATATATTTTTATAATT
1 TTTA-ATATTTTTATAATT
1283388 ATATTTGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 9 0.53
19 4 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTAATATTTTTATAATT
Found at i:1285894 original size:21 final size:20
Alignment explanation
Indices: 1285849--1285894 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
1285839 ACTAAAAATT
*
1285849 AAATAAAATAAATAAACACA
1 AAATTAAATAAATAAACACA
* *
1285869 TAATTAAATAAATTAAACATA
1 AAATTAAATAAA-TAAACACA
1285890 AAATT
1 AAATT
1285895 TAATTAAACC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (20 bp):
AAATTAAATAAATAAACACA
Found at i:1287184 original size:2 final size:2
Alignment explanation
Indices: 1287177--1287207 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1287167 AACATTGATT
*
1287177 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1287208 TGTTGGTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:1287581 original size:16 final size:16
Alignment explanation
Indices: 1287549--1287584 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1287539 TTATTATTAA
*
1287549 TTAATTTAGTAATTAT
1 TTAATTTAGTAAATAT
*
1287565 TTAATTTATTAAATAT
1 TTAATTTAGTAAATAT
1287581 TTAA
1 TTAA
1287585 ATAATTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
TTAATTTAGTAAATAT
Found at i:1287776 original size:10 final size:10
Alignment explanation
Indices: 1287761--1287790 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
1287751 TATTATAATT
1287761 ATTTTATTTA
1 ATTTTATTTA
1287771 ATTTTAATTTA
1 ATTTT-ATTTA
1287782 ATTTTATTT
1 ATTTTATTT
1287791 TTATAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
ATTTTATTTA
Found at i:1288235 original size:12 final size:12
Alignment explanation
Indices: 1288220--1288282 Score: 55
Period size: 12 Copynumber: 5.6 Consensus size: 12
1288210 AATAAATATG
*
1288220 ATAATTTTAAAT
1 ATAATATTAAAT
1288232 ATAATATTAAAT
1 ATAATATTAAAT
*
1288244 ATAAAATT--AT
1 ATAATATTAAAT
1288254 ATAA-ATT-AAT
1 ATAATATTAAAT
*
1288264 ACTAATATTTAAT
1 A-TAATATTAAAT
1288277 A-AATAT
1 ATAATAT
1288283 ATTAATTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
9 3 0.07
10 9 0.20
11 8 0.18
12 21 0.47
13 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
ATAATATTAAAT
Found at i:1288263 original size:27 final size:27
Alignment explanation
Indices: 1288205--1288294 Score: 76
Period size: 27 Copynumber: 3.3 Consensus size: 27
1288195 TCAAATTTTT
* *
1288205 TTAATAATAAATATGATAATT-T-TAAA
1 TTAATATTAAATAT-AAAATTATATAAA
1288231 TATAATATTAAATATAAAATTATATAAA
1 T-TAATATTAAATATAAAATTATATAAA
* * * *
1288259 TTAATACTAATATTTAATAAATATATTAA
1 TTAATATTAA-ATATAA-AATTATATAAA
1288288 TTAATAT
1 TTAATAT
1288295 CCTACATTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
26 6 0.12
27 21 0.40
28 10 0.19
29 15 0.29
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (27 bp):
TTAATATTAAATATAAAATTATATAAA
Found at i:1288568 original size:21 final size:21
Alignment explanation
Indices: 1288527--1288568 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1288517 TACTATTTAT
* *
1288527 TTTAAAAATATATTTACAATA
1 TTTAAAAATATACTTAAAATA
1288548 TTTATAAAAT-TACTTAAAATA
1 TTTA-AAAATATACTTAAAATA
1288569 CTTTTTTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (21 bp):
TTTAAAAATATACTTAAAATA
Found at i:1288686 original size:24 final size:26
Alignment explanation
Indices: 1288625--1288688 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 26
1288615 TATTAAATTT
*
1288625 AATATT-AATTTTTATATAAATTATA
1 AATATTAAATTTTTATACAAATTATA
*
1288650 AATATTTAA-TTTTAT-CAAATTATA
1 AATATTAAATTTTTATACAAATTATA
*
1288674 TA-ATTAAATTTTTAT
1 AATATTAAATTTTTAT
1288689 TATTAATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 5 0.15
24 15 0.44
25 12 0.35
26 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (26 bp):
AATATTAAATTTTTATACAAATTATA
Found at i:1288693 original size:22 final size:22
Alignment explanation
Indices: 1288675--1288717 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1288665 CAAATTATAT
1288675 AATTAAATT-TTTATTATTAATA
1 AATTAAATTATTTA-TATTAATA
1288697 AATTAAATTATTTATATTAAT
1 AATTAAATTATTTATATTAAT
1288718 TTTATTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
AATTAAATTATTTATATTAATA
Found at i:1288855 original size:18 final size:18
Alignment explanation
Indices: 1288832--1288879 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1288822 TTTTTTATTA
1288832 AAATTATATAATAAAATT
1 AAATTATATAATAAAATT
*
1288850 AAATTA-ATAATTAAAGTT
1 AAATTATATAA-TAAAATT
*
1288868 AAATAATATAAT
1 AAATTATATAAT
1288880 TGAAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 4 0.15
18 18 0.69
19 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
AAATTATATAATAAAATT
Found at i:1289103 original size:2 final size:2
Alignment explanation
Indices: 1289096--1289122 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1289086 TTCTTTAGCA
1289096 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1289123 GAAAGTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1290010 original size:11 final size:11
Alignment explanation
Indices: 1289994--1290019 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1289984 ATTGAAGTAC
1289994 ATATATACTAT
1 ATATATACTAT
1290005 ATATATACTAT
1 ATATATACTAT
1290016 ATAT
1 ATAT
1290020 GAAAAAAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (11 bp):
ATATATACTAT
Found at i:1290318 original size:35 final size:32
Alignment explanation
Indices: 1290236--1290318 Score: 78
Period size: 35 Copynumber: 2.3 Consensus size: 32
1290226 ATTAGTGTTT
1290236 AAAAATTAAACAAATAATAATTATAATATTTTTA
1 AAAAATT-AAC-AATAATAATTATAATATTTTTA
1290270 AAAAATTTATAACAATAATTAATTA-AATATAAATTTTA
1 AAAAA--T-TAACAATAA-TAATTATAATAT---TTTTA
1290308 AAAAATTAACA
1 AAAAATTAACA
1290319 GATACCTCCA
Statistics
Matches: 42, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
34 5 0.12
35 15 0.36
36 11 0.26
37 1 0.02
38 10 0.24
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (32 bp):
AAAAATTAACAATAATAATTATAATATTTTTA
Found at i:1291897 original size:28 final size:26
Alignment explanation
Indices: 1291866--1291933 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 26
1291856 TAATTTATTT
**
1291866 AAATAATATTTTTATTTAAATATAATTA
1 AAATAATACATTT-TTT-AATATAATTA
* *
1291894 AAATATATACATTTTTTAATATATTTT
1 AAATA-ATACATTTTTTAATATAATTA
*
1291921 AAATAATAAATTT
1 AAATAATACATTT
1291934 AAATCATTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
26 7 0.21
27 13 0.38
28 8 0.24
29 6 0.18
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (26 bp):
AAATAATACATTTTTTAATATAATTA
Found at i:1291944 original size:14 final size:13
Alignment explanation
Indices: 1291918--1291973 Score: 55
Period size: 12 Copynumber: 4.5 Consensus size: 13
1291908 TTTAATATAT
1291918 TTTAAATAATAAA
1 TTTAAATAATAAA
*
1291931 TTTAAATCATTAAA
1 TTTAAAT-AATAAA
*
1291945 -TTAAATTA-AAA
1 TTTAAATAATAAA
*
1291956 TCTAAAT-ATAAA
1 TTTAAATAATAAA
1291968 TTTAAA
1 TTTAAA
1291974 ATACATAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
11 4 0.11
12 13 0.37
13 13 0.37
14 5 0.14
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (13 bp):
TTTAAATAATAAA
Found at i:1291974 original size:19 final size:20
Alignment explanation
Indices: 1291920--1291981 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 20
1291910 TAATATATTT
1291920 TAAATAATAAATTT-AAATCA
1 TAAAT-ATAAATTTAAAATCA
1291940 TTAAAT-TAAA-TTAAAATC-
1 -TAAATATAAATTTAAAATCA
1291958 TAAATATAAATTTAAAATACA
1 TAAATATAAATTTAAAAT-CA
1291979 TAA
1 TAA
1291982 TAATATTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
17 5 0.14
18 6 0.17
19 16 0.44
20 1 0.03
21 8 0.22
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAATATAAATTTAAAATCA
Found at i:1291976 original size:13 final size:12
Alignment explanation
Indices: 1291879--1291973 Score: 54
Period size: 11 Copynumber: 7.6 Consensus size: 12
1291869 TAATATTTTT
1291879 ATTTAAATAT-A
1 ATTTAAATATAA
*
1291890 ATTAAAATATATA
1 ATTTAAATATA-A
*
1291903 CATTTTTTAATAT-A
1 -A--TTTAAATATAA
*
1291917 TTTTAAATAATAA
1 ATTTAAAT-ATAA
1291930 ATTTAAATCATTAA
1 ATTTAAAT-A-TAA
1291944 A-TTAAAT-TAAA
1 ATTTAAATAT-AA
*
1291955 ATCTAAATATAA
1 ATTTAAATATAA
1291967 ATTTAAA
1 ATTTAAA
1291974 ATACATAATA
Statistics
Matches: 64, Mismatches: 9, Indels: 21
0.68 0.10 0.22
Matches are distributed among these distances:
10 1 0.02
11 18 0.28
12 15 0.23
13 17 0.27
14 6 0.09
16 7 0.11
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (12 bp):
ATTTAAATATAA
Found at i:1292154 original size:23 final size:22
Alignment explanation
Indices: 1292128--1292171 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1292118 TATGCGATGG
1292128 ATAATTAATATTTTAATATATAT
1 ATAATTAAT-TTTTAATATATAT
*
1292151 ATAATTAATTTTTAATTTATA
1 ATAATTAATTTTTAATATATA
1292172 AAAATTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATAATTAATTTTTAATATATAT
Found at i:1292334 original size:73 final size:72
Alignment explanation
Indices: 1292250--1292386 Score: 247
Period size: 73 Copynumber: 1.9 Consensus size: 72
1292240 AACCGTTTAA
*
1292250 ATTCTACTAAAAAGAATTAAAACGTAATTTAAAAAGTAATTAATAAAATTAATATATTATATTAA
1 ATTCTACTAAAAAGAATTAAAACGTAATTTAAAAAATAATTAATAAAATTAATATATTAT-TTAA
1292315 ATTTAATG
65 ATTTAATG
*
1292323 ATTCTACTAAAAAGAATTAAAATGTAATTTAAAAAATAATTAATAAAATTAATATATTATTTAA
1 ATTCTACTAAAAAGAATTAAAACGTAATTTAAAAAATAATTAATAAAATTAATATATTATTTAA
1292387 TGAATGAGAT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
72 4 0.06
73 58 0.94
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (72 bp):
ATTCTACTAAAAAGAATTAAAACGTAATTTAAAAAATAATTAATAAAATTAATATATTATTTAAA
TTTAATG
Found at i:1292385 original size:32 final size:35
Alignment explanation
Indices: 1292349--1292418 Score: 92
Period size: 36 Copynumber: 2.1 Consensus size: 35
1292339 TTAAAATGTA
1292349 ATTTAAAAAAT-A-ATT-AATAAAATTAATATATT
1 ATTTAAAAAATGAGATTAAATAAAATTAATATATT
**
1292381 ATTTAATGAATGAGATTGAAATAAAATTAATATATT
1 ATTTAAAAAATGAGATT-AAATAAAATTAATATATT
1292417 AT
1 AT
1292419 ATTATACACA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 9 0.28
33 1 0.03
34 3 0.09
36 19 0.59
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (35 bp):
ATTTAAAAAATGAGATTAAATAAAATTAATATATT
Found at i:1292450 original size:9 final size:9
Alignment explanation
Indices: 1292428--1292471 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
1292418 TATTATACAC
1292428 AATAAATAAA
1 AATAAAT-AA
1292438 AATAAATAA
1 AATAAATAA
1292447 AATAAAT-A
1 AATAAATAA
*
1292455 AATAAATTA
1 AATAAATAA
*
1292464 AATTAATA
1 AATAAATA
1292472 TTATAAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
8 8 0.26
9 16 0.52
10 7 0.23
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (9 bp):
AATAAATAA
Found at i:1292455 original size:13 final size:13
Alignment explanation
Indices: 1292437--1292471 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1292427 CAATAAATAA
1292437 AAATAAATAAAAT
1 AAATAAATAAAAT
*
1292450 AAATAAATAAATT
1 AAATAAATAAAAT
*
1292463 AAATTAATA
1 AAATAAATA
1292472 TTATAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:1296625 original size:24 final size:24
Alignment explanation
Indices: 1296598--1296648 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
1296588 ATCTGATAAA
* * *
1296598 GCTGATAAAGCTGCTGCTGCGGCT
1 GCTGATAAAGCAGATGCTGCCGCT
* *
1296622 GCTGCTGAAGCAGATGCTGCCGCT
1 GCTGATAAAGCAGATGCTGCCGCT
1296646 GCT
1 GCT
1296649 ACTTTGGCTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.16, C:0.27, G:0.33, T:0.24
Consensus pattern (24 bp):
GCTGATAAAGCAGATGCTGCCGCT
Found at i:1305816 original size:25 final size:26
Alignment explanation
Indices: 1305788--1305841 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
1305778 AATTATCGTC
*
1305788 TTTTTTA-AT-AAATATAATAATTAAA
1 TTTTTTATATCAAATA-AATAATAAAA
1305813 -TTTTTATATCAAATAAATAATAAAA
1 TTTTTTATATCAAATAAATAATAAAA
1305838 TTTT
1 TTTT
1305842 ATTTAATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
24 6 0.24
25 11 0.44
26 8 0.32
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
TTTTTTATATCAAATAAATAATAAAA
Found at i:1305842 original size:24 final size:25
Alignment explanation
Indices: 1305790--1305843 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
1305780 TTATCGTCTT
*
1305790 TTTTA-ATAAATATAATAATTAAAT
1 TTTTATATAAATATAATAATTAAAA
1305814 TTTTATATCAAATA-AATAA-TAAAA
1 TTTTATAT-AAATATAATAATTAAAA
1305838 TTTTAT
1 TTTTAT
1305844 TTAATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 15 0.56
25 7 0.26
26 5 0.19
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TTTTATATAAATATAATAATTAAAA
Found at i:1305913 original size:15 final size:16
Alignment explanation
Indices: 1305885--1305917 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1305875 TAAATAGTGT
1305885 ATAAAATATAATAAAA
1 ATAAAATATAATAAAA
*
1305901 ATAAATTAT-ATAAAA
1 ATAAAATATAATAAAA
1305916 AT
1 AT
1305918 TATAAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAAAATATAATAAAA
Found at i:1306919 original size:17 final size:17
Alignment explanation
Indices: 1306899--1306949 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
1306889 ATAATTATTT
1306899 TAATAAAAATTAAATAA
1 TAATAAAAATTAAATAA
*
1306916 TAATAATAATTTAAA-AA
1 TAATAA-AAATTAAATAA
*
1306933 TATTATAAAATATAAAT
1 TAATA-AAAAT-TAAAT
1306950 TTTTAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TAATAAAAATTAAATAA
Found at i:1306920 original size:29 final size:28
Alignment explanation
Indices: 1306875--1306960 Score: 81
Period size: 29 Copynumber: 3.1 Consensus size: 28
1306865 TTATTAAAAT
* *
1306875 AAAATAAAATAAAAATAATTATTTTAATA
1 AAAATTAAATAATAATAA-TATTTTAATA
*
1306904 AAAATTAAATAATAATAATAATTTAA-A
1 AAAATTAAATAATAATAATATTTTAATA
*
1306931 AATATTATAA-AAT-ATAA-ATTTTTAATA
1 AAAATTA-AATAATAATAATA-TTTTAATA
1306958 AAA
1 AAA
1306961 TAATTTAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
25 1 0.02
26 9 0.19
27 13 0.27
28 9 0.19
29 16 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (28 bp):
AAAATTAAATAATAATAATATTTTAATA
Found at i:1306971 original size:21 final size:21
Alignment explanation
Indices: 1306913--1306976 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
1306903 AAAAATTAAA
* *
1306913 TAATAATAATAATTTAAAAATAT
1 TAATAA-AATAATTT-AAATTTT
1306936 T-ATAAAAT-A--TAAATTTT
1 TAATAAAATAATTTAAATTTT
1306953 TAATAAAATAATTTAAATTTT
1 TAATAAAATAATTTAAATTTT
1306974 TAA
1 TAA
1306977 AATAATTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
17 6 0.17
18 8 0.23
19 1 0.03
20 1 0.03
21 14 0.40
22 4 0.11
23 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAATAAAATAATTTAAATTTT
Found at i:1307412 original size:19 final size:19
Alignment explanation
Indices: 1307376--1307413 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1307366 CGTAAAATAA
*
1307376 AAAAAATATTTATAAAAAT
1 AAAAAATATTAATAAAAAT
*
1307395 AAAAAATATTAATTAAAAT
1 AAAAAATATTAATAAAAAT
1307414 GATCGTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAAATATTAATAAAAAT
Found at i:1309059 original size:5 final size:5
Alignment explanation
Indices: 1309049--1309098 Score: 73
Period size: 5 Copynumber: 10.0 Consensus size: 5
1309039 CTTGAGAACT
* * *
1309049 AGCCC AGCCC AGCCC AGCCC AGCCC AGCCC AGCCC TGCCC TGCCC TGCCC
1 AGCCC AGCCC AGCCC AGCCC AGCCC AGCCC AGCCC AGCCC AGCCC AGCCC
1309099 CTTCAATTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 44 1.00
ACGTcount: A:0.14, C:0.60, G:0.20, T:0.06
Consensus pattern (5 bp):
AGCCC
Found at i:1309685 original size:16 final size:16
Alignment explanation
Indices: 1309664--1309711 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1309654 AATAATAAAT
1309664 AATTTATTTTTTAATA
1 AATTTATTTTTTAATA
* *
1309680 AATTTATTTGTGAATA
1 AATTTATTTTTTAATA
*
1309696 AA-CTATTTATTTAATA
1 AATTTATTT-TTTAATA
1309712 CATAAAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 5 0.19
16 21 0.81
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (16 bp):
AATTTATTTTTTAATA
Found at i:1310245 original size:27 final size:26
Alignment explanation
Indices: 1310205--1310255 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
1310195 TGAATTTAAT
* *
1310205 TATTATTTAAAATATACATTATAAAAA
1 TATTAATTAAAATATAAATT-TAAAAA
*
1310232 TATTAATTACAATATAAATTTAAA
1 TATTAATTAAAATATAAATTTAAA
1310256 TGTATATCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 4 0.19
27 17 0.81
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (26 bp):
TATTAATTAAAATATAAATTTAAAAA
Found at i:1310505 original size:2 final size:2
Alignment explanation
Indices: 1310493--1310527 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1310483 CATATTTTAC
1310493 AT AT AT A- 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
1310528 TTGTAGCAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1313072 original size:3 final size:3
Alignment explanation
Indices: 1313066--1313097 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1313056 TGCAAGATTG
1313066 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1313098 CCATCTGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1318392 original size:2 final size:2
Alignment explanation
Indices: 1318372--1318418 Score: 60
Period size: 2 Copynumber: 23.5 Consensus size: 2
1318362 AATAATCCAC
* *
1318372 TA TA CA TA TA -A TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TT
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1318414 TA TA T
1 TA TA T
1318419 TCCTTTCTGG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.92
3 2 0.05
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1318486 original size:3 final size:3
Alignment explanation
Indices: 1318480--1318505 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1318470 GGCACTTTAA
1318480 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1318506 AAGTAGGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1318935 original size:30 final size:27
Alignment explanation
Indices: 1318900--1318976 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 27
1318890 ATTTTTATAT
1318900 TTTATAATTATTTATTTAAAATATTAAATA
1 TTTAT-ATTATTTATTTAAAA-ATT-AATA
* *
1318930 TTTATATTAATT-TTTATAAATTAATA
1 TTTATATTATTTATTTAAAAATTAATA
*
1318956 TTCATATTATATATATTTAAA
1 TTTATATTAT-T-TATTTAAA
1318977 TATGATTATA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 12 0.31
27 4 0.10
28 7 0.18
29 11 0.28
30 5 0.13
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (27 bp):
TTTATATTATTTATTTAAAAATTAATA
Found at i:1319040 original size:27 final size:28
Alignment explanation
Indices: 1318984--1319042 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
1318974 AAATATGATT
* *
1318984 ATATTTTATTTTATATTTTAATTTTTTA
1 ATATTTTATTTTATATTATAATTTTATA
1319012 ATATTTTA-TTTATATTAT-ATTATTATA
1 ATATTTTATTTTATATTATAATT-TTATA
1319039 ATAT
1 ATAT
1319043 GATCGTATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 3 0.11
27 17 0.61
28 8 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (28 bp):
ATATTTTATTTTATATTATAATTTTATA
Found at i:1324233 original size:18 final size:20
Alignment explanation
Indices: 1324207--1324249 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
1324197 TACGATTGTT
*
1324207 TAATGTTTTAAT-TAA-TAA
1 TAATTTTTTAATCTAATTAA
1324225 TAATTTTTTAATCTAATTAA
1 TAATTTTTTAATCTAATTAA
1324245 TAATT
1 TAATT
1324250 AATTTTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.50
19 3 0.14
20 8 0.36
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
TAATTTTTTAATCTAATTAA
Found at i:1325404 original size:17 final size:17
Alignment explanation
Indices: 1325378--1325421 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
1325368 CTTAATATGA
1325378 AAATAAATATTTAATAT
1 AAATAAATATTTAATAT
*
1325395 AAATACATATTTAATAT
1 AAATAAATATTTAATAT
1325412 --ATAAATATTT
1 AAATAAATATTT
1325422 TTACATTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 9 0.36
17 16 0.64
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATAAATATTTAATAT
Found at i:1325941 original size:2 final size:2
Alignment explanation
Indices: 1325934--1325972 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1325924 ATACATGTGC
1325934 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1325973 CAGAACTTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1327747 original size:3 final size:3
Alignment explanation
Indices: 1327741--1327801 Score: 104
Period size: 3 Copynumber: 20.3 Consensus size: 3
1327731 TTTTTTGGGG
*
1327741 AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
1327789 AGT AAT AAT AAT A
1 AAT AAT AAT AAT A
1327802 TGAAGTTGAG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1330000 original size:2 final size:2
Alignment explanation
Indices: 1329995--1330024 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1329985 AAAAACGTGC
1329995 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
1330025 TTATTGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1331105 original size:16 final size:16
Alignment explanation
Indices: 1331084--1331115 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1331074 ATGTTTAAAC
1331084 ACAATCTTTATCTATA
1 ACAATCTTTATCTATA
*
1331100 ACAATCTTTATTTATA
1 ACAATCTTTATCTATA
1331116 GAGCTACATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.47
Consensus pattern (16 bp):
ACAATCTTTATCTATA
Found at i:1340891 original size:2 final size:2
Alignment explanation
Indices: 1340884--1340913 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1340874 CGGAAGCGGT
1340884 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1340914 AGAAGACTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1342707 original size:11 final size:11
Alignment explanation
Indices: 1342691--1342732 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
1342681 ATATATTTAA
1342691 ATATTTATTTT
1 ATATTTATTTT
1342702 ATATTTATTTT
1 ATATTTATTTT
*
1342713 TTAATTATATTTT
1 AT-ATT-TATTTT
1342726 ATATTTA
1 ATATTTA
1342733 AATATAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 14 0.52
12 6 0.22
13 7 0.26
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
ATATTTATTTT
Found at i:1342714 original size:13 final size:13
Alignment explanation
Indices: 1342678--1342732 Score: 53
Period size: 13 Copynumber: 4.3 Consensus size: 13
1342668 TAAATAAAAT
*
1342678 TTTATATATTTAAA
1 TTTATAT-TTTATA
1342692 TATT-TATTTTATA
1 T-TTATATTTTATA
1342705 TTTAT-TTTT-TA
1 TTTATATTTTATA
*
1342716 ATTATATTTTATA
1 TTTATATTTTATA
1342729 TTTA
1 TTTA
1342733 AATATAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
11 6 0.18
12 10 0.29
13 12 0.35
14 4 0.12
15 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTATATTTTATA
Found at i:1347655 original size:15 final size:15
Alignment explanation
Indices: 1347635--1347699 Score: 58
Period size: 15 Copynumber: 4.1 Consensus size: 15
1347625 ATTTTTTTAA
1347635 AAATTAATATAATAT
1 AAATTAATATAATAT
* *
1347650 AAATTATTATTATAT
1 AAATTAATATAATAT
*
1347665 CATAATTTATATAATAT
1 -A-AATTAATATAATAT
* *
1347682 AAAATATTATAAATAT
1 AAATTAATAT-AATAT
1347698 AA
1 AA
1347700 TTCTAATATT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
15 19 0.49
16 9 0.23
17 11 0.28
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
AAATTAATATAATAT
Found at i:1352844 original size:25 final size:24
Alignment explanation
Indices: 1352816--1352865 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
1352806 ATTATATATT
1352816 TAAATTTTATATTTAAAAT-TAAAAA
1 TAAATTTTA-A-TTAAAATGTAAAAA
*
1352841 TAAATTTTAATTATAATGTAAAAA
1 TAAATTTTAATTAAAATGTAAAAA
1352865 T
1 T
1352866 TTATTTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 6 0.26
24 8 0.35
25 9 0.39
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
TAAATTTTAATTAAAATGTAAAAA
Found at i:1353156 original size:23 final size:21
Alignment explanation
Indices: 1353129--1353218 Score: 75
Period size: 17 Copynumber: 4.3 Consensus size: 21
1353119 ACTATTTTAA
1353129 ATATATGAAAAATAAAAAATAT
1 ATATAT-AAAAATAAAAAATAT
1353151 GATATA-AAAAATAATTAAAATAT
1 -ATATATAAAAATAA--AAAATAT
1353174 A-ATATAAAAAT---AAATAT
1 ATATATAAAAATAAAAAATAT
*
1353191 -TATATAAATATAAAAACATAT
1 ATATATAAAAATAAAAA-ATAT
*
1353212 AAATATA
1 ATATATA
1353219 TATGTGTAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 19
0.73 0.03 0.25
Matches are distributed among these distances:
17 15 0.27
20 2 0.04
21 15 0.27
22 12 0.21
23 12 0.21
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (21 bp):
ATATATAAAAATAAAAAATAT
Found at i:1353160 original size:21 final size:20
Alignment explanation
Indices: 1353131--1353218 Score: 74
Period size: 21 Copynumber: 4.2 Consensus size: 20
1353121 TATTTTAAAT
*
1353131 ATATGAAAAATAAAAAATATG
1 ATAT-AAAAATAAAAAATATA
1353152 ATATAAAAAATAATTAAAATATA
1 ATAT-AAAAATAA--AAAATATA
*
1353175 ATATAAAAAT---AAATATT
1 ATATAAAAATAAAAAATATA
*
1353192 ATATAAATATAAAAACATATAA
1 ATATAAAAATAAAAA-ATAT-A
1353214 ATATA
1 ATATA
1353219 TATGTGTAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
17 15 0.27
20 2 0.04
21 16 0.29
22 11 0.20
23 11 0.20
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (20 bp):
ATATAAAAATAAAAAATATA
Found at i:1353175 original size:11 final size:12
Alignment explanation
Indices: 1353139--1353240 Score: 61
Period size: 12 Copynumber: 8.7 Consensus size: 12
1353129 ATATATGAAA
*
1353139 AATAAAAAATAT
1 AATATAAAATAT
* *
1353151 GATATAAAAAAT
1 AATATAAAATAT
1353163 AAT-TAAAATAT
1 AATATAAAATAT
1353174 AATATAAAA-AT
1 AATATAAAATAT
**
1353185 AA-ATATTATAT
1 AATATAAAATAT
1353196 AAATATAAAA-A-
1 -AATATAAAATAT
*
1353207 CATATAAATATAT
1 AATATAAA-ATAT
* *
1353220 ATGTGTAAAATAT
1 A-ATATAAAATAT
*
1353233 TATATAAA
1 AATATAAA
1353241 TTTATAATAC
Statistics
Matches: 66, Mismatches: 16, Indels: 16
0.67 0.16 0.16
Matches are distributed among these distances:
10 11 0.17
11 17 0.26
12 25 0.38
13 8 0.12
14 5 0.08
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (12 bp):
AATATAAAATAT
Found at i:1353182 original size:22 final size:22
Alignment explanation
Indices: 1353131--1353220 Score: 78
Period size: 23 Copynumber: 4.0 Consensus size: 22
1353121 TATTTTAAAT
* *
1353131 ATATGAAAAATAA-AAAATATG
1 ATATAAAAAATAATAAAATATA
1353152 ATATAAAAAATAATTAAAATATA
1 ATATAAAAAATAA-TAAAATATA
**
1353175 ATAT-AAAAATAAATATTATATAA
1 ATATAAAAAAT-AATAAAATAT-A
1353198 ATATAAAAACAT-ATAAATATATA
1 ATATAAAAA-ATAATAAA-ATATA
1353221 TGTGTAAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
21 12 0.21
22 12 0.21
23 22 0.39
24 8 0.14
25 2 0.04
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (22 bp):
ATATAAAAAATAATAAAATATA
Found at i:1353469 original size:18 final size:19
Alignment explanation
Indices: 1353430--1353474 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
1353420 TTATATAGTT
*
1353430 AATTTTATATTATTAATAA
1 AATTTTATATTATAAATAA
1353449 AATTTTA-ATTATAAA-ATA
1 AATTTTATATTATAAATA-A
1353467 AATTTTAT
1 AATTTTAT
1353475 TAAATAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 1 0.04
18 15 0.65
19 7 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AATTTTATATTATAAATAA
Found at i:1353483 original size:17 final size:19
Alignment explanation
Indices: 1353430--1353484 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 19
1353420 TTATATAGTT
1353430 AATTTTATATTAT--TAATAA
1 AATTTTA-ATTATAATAAT-A
1353449 AATTTTAATTATAA-AATA
1 AATTTTAATTATAATAATA
1353467 AATTTT-ATTA-AATAATA
1 AATTTTAATTATAATAATA
1353484 A
1 A
1353485 TTATGTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
16 2 0.06
17 9 0.27
18 12 0.36
19 10 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATTTTAATTATAATAATA
Found at i:1353851 original size:17 final size:19
Alignment explanation
Indices: 1353831--1353875 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 19
1353821 AAATAATTAA
1353831 AAAACTAATATAAA-A-AT
1 AAAACTAATATAAATATAT
*
1353848 AAAATTAATATAAATATTAT
1 AAAACTAATATAAATA-TAT
1353868 AAAACTAA
1 AAAACTAA
1353876 AATATATGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 13 0.57
18 1 0.04
20 9 0.39
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAACTAATATAAATATAT
Found at i:1358709 original size:22 final size:21
Alignment explanation
Indices: 1358684--1358736 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
1358674 AATCAAATTA
1358684 ATAAAATTTAATTCAATTTTAT
1 ATAAAATTTAATTCAATTTT-T
* *
1358706 ATAATATTTAATTTAATTTTT
1 ATAAAATTTAATTCAATTTTT
1358727 -TAAAATTTAA
1 ATAAAATTTAA
1358737 AATATTACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 9 0.32
21 1 0.04
22 18 0.64
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
ATAAAATTTAATTCAATTTTT
Found at i:1359978 original size:25 final size:24
Alignment explanation
Indices: 1359966--1360041 Score: 82
Period size: 26 Copynumber: 3.0 Consensus size: 24
1359956 TTATATAATG
1359966 TAAAATATTATATAAATAAATATAT
1 TAAAAT-TTATATAAATAAATATAT
1359991 TAAAATTTATATTAATATAAAT-TAT
1 TAAAATTTATA-TAA-ATAAATATAT
*
1360016 TAATAATTTAATAAAATATAAATATA
1 TAA-AATTT-ATATAA-ATAAATATA
1360042 CGAATACAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
24 5 0.11
25 15 0.33
26 20 0.44
27 5 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TAAAATTTATATAAATAAATATAT
Found at i:1359990 original size:17 final size:17
Alignment explanation
Indices: 1359942--1359992 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
1359932 ACCATAATTT
1359942 TAAATAAAATATAATTATA
1 TAAAT-AAATAT-ATTATA
*
1359961 TAATGTAAA-ATATTATA
1 TAA-ATAAATATATTATA
1359978 TAAATAAATATATTA
1 TAAATAAATATATTA
1359993 AAATTTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 4 0.14
17 15 0.54
18 2 0.07
19 6 0.21
20 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
TAAATAAATATATTATA
Found at i:1363171 original size:3 final size:3
Alignment explanation
Indices: 1363165--1363194 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1363155 GGAGGATAAT
1363165 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC
1 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC
1363195 GTGTCTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.33, T:0.00
Consensus pattern (3 bp):
AGC
Found at i:1364011 original size:27 final size:26
Alignment explanation
Indices: 1363962--1364012 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
1363952 TTTGTTTATT
*
1363962 AATATTAATTAAAATGTTATTAAAAA
1 AATATTAATTAAAATATTATTAAAAA
* *
1363988 AATATATAATTAATATATTTTTAAA
1 AATAT-TAATTAAAATATTATTAAA
1364013 TTTAATAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 5 0.24
27 16 0.76
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (26 bp):
AATATTAATTAAAATATTATTAAAAA
Found at i:1364645 original size:21 final size:22
Alignment explanation
Indices: 1364612--1364660 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
1364602 TAATAAATCA
1364612 ATTTAATTGAATTTAAAATT-TT
1 ATTTAATTGAA-TTAAAATTATT
*
1364634 ATTTAATT-AATTAATATTATT
1 ATTTAATTGAATTAAAATTATT
1364655 ATTTAA
1 ATTTAA
1364661 AATAATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 7 0.28
21 10 0.40
22 8 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
ATTTAATTGAATTAAAATTATT
Found at i:1371587 original size:22 final size:22
Alignment explanation
Indices: 1371562--1371611 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1371552 TTTAATATAA
* *
1371562 ATATATTTATTTTTTAT-TTTTT
1 ATATATTT-TTATTTATATTTAT
1371584 ATATATTTTTATTTATATTTAT
1 ATATATTTTTATTTATATTTAT
1371606 ATATAT
1 ATATAT
1371612 ATATATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
ATATATTTTTATTTATATTTAT
Found at i:1371594 original size:10 final size:10
Alignment explanation
Indices: 1371569--1371620 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 10
1371559 TAAATATATT
1371569 TATTTTT-TA
1 TATTTTTATA
1371578 T-TTTTTATA
1 TATTTTTATA
*
1371587 TATTTTTATT
1 TATTTTTATA
*
1371597 TATATTTATA
1 TATTTTTATA
* *
1371607 TATATATATA
1 TATTTTTATA
1371617 TATT
1 TATT
1371621 AAATATAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
8 5 0.14
9 4 0.11
10 27 0.75
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TATTTTTATA
Found at i:1371604 original size:6 final size:6
Alignment explanation
Indices: 1371563--1371620 Score: 50
Period size: 6 Copynumber: 10.0 Consensus size: 6
1371553 TTAATATAAA
* * *
1371563 TATATT TAT-TT TTTATT T-T-TT ATATATT TTTATT TATATT TATATA
1 TATATT TATATT TATATT TATATT -TATATT TATATT TATATT TATATT
*
1371609 TATATA TATATT
1 TATATT TATATT
1371621 AAATATAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
4 2 0.05
5 6 0.14
6 33 0.77
7 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TATATT
Found at i:1371631 original size:16 final size:16
Alignment explanation
Indices: 1371597--1371644 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
1371587 TATTTTTATT
*
1371597 TATAT-TTATATATATA
1 TATATATTAAATATA-A
1371613 TATATATTAAATATAA
1 TATATATTAAATATAA
1371629 TATA-ATATAAATATAA
1 TATATAT-TAAATATAA
1371645 AAAATAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 2 0.07
16 19 0.66
17 8 0.28
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATATATTAAATATAA
Found at i:1371642 original size:23 final size:24
Alignment explanation
Indices: 1371604--1371652 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
1371594 ATTTATATTT
* * *
1371604 ATATATATATATATATTAAATATA
1 ATATATATATAAATATAAAAAATA
1371628 ATATA-ATATAAATATAAAAAATA
1 ATATATATATAAATATAAAAAATA
1371651 AT
1 AT
1371653 TAAAAATCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
ATATATATATAAATATAAAAAATA
Found at i:1373929 original size:21 final size:22
Alignment explanation
Indices: 1373883--1373929 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
1373873 TCCAATAATC
* * *
1373883 AAATAATTTTTAAAGAATATTT
1 AAATAAGTTTCAAAGAAAATTT
1373905 -AATAAGTTTCAAA-AAAATTT
1 AAATAAGTTTCAAAGAAAATTT
1373925 AAATA
1 AAATA
1373930 TAAAAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.38
Consensus pattern (22 bp):
AAATAAGTTTCAAAGAAAATTT
Found at i:1374031 original size:4 final size:4
Alignment explanation
Indices: 1374019--1374049 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
1374009 TAAATTGAAT
1374019 ATAA TATAA ATAA ATAA ATAA ATAA ATAA AT
1 ATAA -ATAA ATAA ATAA ATAA ATAA ATAA AT
1374050 GAAGACGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (4 bp):
ATAA
Found at i:1377135 original size:11 final size:11
Alignment explanation
Indices: 1377119--1377159 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 11
1377109 AGATAATATC
1377119 TTTTAAAAATA
1 TTTTAAAAATA
*
1377130 TTTTAAATATA
1 TTTTAAAAATA
*
1377141 -TATAAAAA-A
1 TTTTAAAAATA
1377150 TTTTAAAAAT
1 TTTTAAAAAT
1377160 TAAATATACT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
9 1 0.04
10 13 0.54
11 10 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TTTTAAAAATA
Found at i:1378581 original size:21 final size:21
Alignment explanation
Indices: 1378523--1378582 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
1378513 TAAACTTGTA
*
1378523 TTTA-TTTATAAATTAATATT
1 TTTATTTTATAAATAAATATT
* *
1378543 TGATATATTGAT-AATAAATATT
1 T-TTAT-TTTATAAATAAATATT
1378565 TTTATTTTATAAATAAAT
1 TTTATTTTATAAATAAAT
1378583 TAAAAAGCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
20 5 0.16
21 12 0.39
22 10 0.32
23 4 0.13
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (21 bp):
TTTATTTTATAAATAAATATT
Found at i:1386574 original size:19 final size:22
Alignment explanation
Indices: 1386536--1386587 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
1386526 CACTTACAGA
*
1386536 ATTTATTATAAATAATTTATTT
1 ATTTATTATAAATAATTTATAT
1386558 ATTTATT-T-AATAA-TTATAT
1 ATTTATTATAAATAATTTATAT
1386577 ATTTTATTATA
1 A-TTTATTATA
1386588 TTATAATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 6 0.23
20 11 0.42
21 2 0.08
22 7 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTATTATAAATAATTTATAT
Found at i:1386582 original size:20 final size:20
Alignment explanation
Indices: 1386546--1386623 Score: 60
Period size: 20 Copynumber: 4.1 Consensus size: 20
1386536 ATTTATTATA
*
1386546 AATAATT-TATTTATTTATTT
1 AATAATTATATAT-TTTATTT
1386566 AATAATTATATATTTTA-TT
1 AATAATTATATATTTTATTT
*
1386585 -AT-ATTATA-ATTATATTT
1 AATAATTATATATTTTATTT
* *
1386602 AAAATATTTTATA-TTTATTT
1 AATA-ATTATATATTTTATTT
1386622 AA
1 AA
1386624 ATTTTAATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
16 5 0.11
17 8 0.17
18 3 0.06
19 2 0.04
20 24 0.51
21 5 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
AATAATTATATATTTTATTT
Found at i:1386586 original size:23 final size:24
Alignment explanation
Indices: 1386555--1386599 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
1386545 AAATAATTTA
1386555 TTTATTTAT-TTAATAATTATATAT
1 TTTATTTATATT-ATAATTATATAT
1386579 TTTA-TTATATTATAATTATAT
1 TTTATTTATATTATAATTATAT
1386600 TTAAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTATTTATATTATAATTATATAT
Found at i:1396347 original size:2 final size:2
Alignment explanation
Indices: 1396340--1396366 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1396330 AAAATAACAA
1396340 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1396367 AATCTCTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1405185 original size:76 final size:75
Alignment explanation
Indices: 1405099--1405253 Score: 247
Period size: 76 Copynumber: 2.1 Consensus size: 75
1405089 TAATCAGCCA
*
1405099 TACTCTATTCTAATAAACGAGCCTAACTCCGGGTTTTACTAACCATTTTCTACTTTCAATCAGCC
1 TACTCTATTCTAATAAACGAGCCAAACTCCGGGTTTTACTAACCATTTT-TACTTTCAATCAGCC
1405164 ATTTTTTGGGC
65 ATTTTTTGGGC
* * * * *
1405175 TACTCTATTCTAATAAAGGAGCCAAACTCCGGGTTTTAGTAGCCGTTTTTACTTTCAATCAGTCA
1 TACTCTATTCTAATAAACGAGCCAAACTCCGGGTTTTACTAACCATTTTTACTTTCAATCAGCCA
1405240 TTTTTTGGGC
66 TTTTTTGGGC
1405250 TACT
1 TACT
1405254 AACCAACAGG
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
75 29 0.40
76 44 0.60
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.39
Consensus pattern (75 bp):
TACTCTATTCTAATAAACGAGCCAAACTCCGGGTTTTACTAACCATTTTTACTTTCAATCAGCCA
TTTTTTGGGC
Found at i:1406008 original size:2 final size:2
Alignment explanation
Indices: 1406001--1406027 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1405991 TTTACAAATG
1406001 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1406028 GATCATGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1406500 original size:23 final size:22
Alignment explanation
Indices: 1406449--1406501 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
1406439 ATTTGTTTTT
* *
1406449 AATTAAAAAAAAATCACTTTAA
1 AATTAAAAAAAAATAAATTTAA
*
1406471 AGA-TAAAAAAAAGTAAATATTAA
1 A-ATTAAAAAAAAATAAAT-TTAA
1406494 AATTAAAA
1 AATTAAAA
1406502 TTAAAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (22 bp):
AATTAAAAAAAAATAAATTTAA
Found at i:1407352 original size:28 final size:27
Alignment explanation
Indices: 1407316--1407391 Score: 80
Period size: 29 Copynumber: 2.7 Consensus size: 27
1407306 AAAATAATAA
* * **
1407316 TAAAAAAATCTTTACATTTTATAATTTT
1 TAAATAAATTTTTA-ATTTTATAATACT
*
1407344 TAAATAAATTTTTATATTTTTATTATACT
1 TAAATAAATTTTTA-A-TTTTATAATACT
1407373 TAAATAAATTTTTAATTTT
1 TAAATAAATTTTTAATTTT
1407392 TATTCATATA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
27 4 0.10
28 14 0.34
29 23 0.56
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (27 bp):
TAAATAAATTTTTAATTTTATAATACT
Found at i:1407375 original size:29 final size:28
Alignment explanation
Indices: 1407343--1407425 Score: 105
Period size: 29 Copynumber: 2.9 Consensus size: 28
1407333 TTTATAATTT
1407343 TTAAATAAATTTTTATATTTTTATT-ATA
1 TTAAATAAATTTTTA-ATTTTTATTCATA
1407371 CTTAAATAAATTTTTAATTTTTATTCATA
1 -TTAAATAAATTTTTAATTTTTATTCATA
* *
1407400 TAAATATATAACTTTTAATTTTTATT
1 TTAA-ATA-AATTTTTAATTTTTATT
1407426 TGAACAAACT
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
28 12 0.24
29 21 0.43
30 16 0.33
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.58
Consensus pattern (28 bp):
TTAAATAAATTTTTAATTTTTATTCATA
Found at i:1414753 original size:14 final size:14
Alignment explanation
Indices: 1414734--1414760 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1414724 TATGCTCTGG
1414734 AGAAGGTTTTTAAA
1 AGAAGGTTTTTAAA
1414748 AGAAGGTTTTTAA
1 AGAAGGTTTTTAA
1414761 CTCTTATGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (14 bp):
AGAAGGTTTTTAAA
Found at i:1418837 original size:24 final size:24
Alignment explanation
Indices: 1418810--1418856 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1418800 AATTTATAAA
** *
1418810 TTTAATTTTTTATATTAATATTAT
1 TTTAATTAATTATAATAATATTAT
1418834 TTTAATTAATTATAATAATATTA
1 TTTAATTAATTATAATAATATTA
1418857 ATTACATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTAATTAATTATAATAATATTAT
Found at i:1420146 original size:2 final size:2
Alignment explanation
Indices: 1420134--1420168 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1420124 TTAATAAATT
*
1420134 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1420169 TCGGGAGCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1420769 original size:2 final size:2
Alignment explanation
Indices: 1420762--1420796 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1420752 ATATCTAGGT
1420762 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1420797 TTCACTTGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1423802 original size:14 final size:14
Alignment explanation
Indices: 1423785--1423814 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1423775 TTATTTTTAA
*
1423785 AAATTTAATAATTT
1 AAATCTAATAATTT
1423799 AAATCTAATAATTT
1 AAATCTAATAATTT
1423813 AA
1 AA
1423815 GCTTTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATCTAATAATTT
Found at i:1426180 original size:19 final size:22
Alignment explanation
Indices: 1426153--1426206 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
1426143 TTTTTTCCAT
*
1426153 TTATCAAATATTTTT-AAATAA
1 TTATAAAATATTTTTAAAATAA
1426174 -TA-AAAATAATTTTTTAAAATAA
1 TTATAAAAT-A-TTTTTAAAATAA
1426196 TTATAAAATAT
1 TTATAAAATAT
1426207 ATAATTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
19 4 0.15
20 3 0.11
21 5 0.19
22 7 0.26
23 3 0.11
24 5 0.19
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
TTATAAAATATTTTTAAAATAA
Found at i:1426188 original size:22 final size:22
Alignment explanation
Indices: 1426163--1426236 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
1426153 TTATCAAATA
1426163 TTTTTAAATAATAAAAATAATT
1 TTTTTAAATAATAAAAATAATT
* *
1426185 TTTTAAAATAATTATAAAATATATAA
1 TTTTTAAATAA-TA-AAAATA-AT-T
*
1426211 TTATT-AAT-ATAAAAAT-ATT
1 TTTTTAAATAATAAAAATAATT
1426230 TTTTTAA
1 TTTTTAA
1426237 TATTTTTAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
19 4 0.10
20 3 0.07
22 15 0.37
23 4 0.10
24 7 0.17
25 5 0.12
26 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TTTTTAAATAATAAAAATAATT
Found at i:1427965 original size:21 final size:21
Alignment explanation
Indices: 1427924--1427965 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1427914 AGTACGATCC
*
1427924 CAACAACAACGACGACAGGCA
1 CAACAACAACGACAACAGGCA
* *
1427945 CAACAGCAACGACAACCGGCA
1 CAACAACAACGACAACAGGCA
1427966 GCACGACATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.36, G:0.19, T:0.00
Consensus pattern (21 bp):
CAACAACAACGACAACAGGCA
Found at i:1428266 original size:3 final size:3
Alignment explanation
Indices: 1428258--1428303 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1428248 AAAACAAGAC
1428258 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1428304 TTGCTTTTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1428656 original size:2 final size:2
Alignment explanation
Indices: 1428649--1428676 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1428639 AAAGTGTTAA
1428649 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
1428677 TTCAATAAAA
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:1428984 original size:20 final size:20
Alignment explanation
Indices: 1428959--1429000 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1428949 TTAATACAAG
1428959 TGCATGAACTTACTTATACA
1 TGCATGAACTTACTTATACA
1428979 TGCATGAACTTACTTATACA
1 TGCATGAACTTACTTATACA
1428999 TG
1 TG
1429001 TAATTTGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (20 bp):
TGCATGAACTTACTTATACA
Found at i:1440801 original size:36 final size:36
Alignment explanation
Indices: 1440752--1440830 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
1440742 TAAGGCACAG
* * *
1440752 AAAAAAAATTCAATATGGCTGCAAGAAACTCATTTA
1 AAAAAAAAATCAATATGGCAGCAAGAAACTCATCTA
*
1440788 AAAAAAAAATCAATATGGCAGCAAGAAGCTCATCTA
1 AAAAAAAAATCAATATGGCAGCAAGAAACTCATCTA
1440824 AAAAAAA
1 AAAAAAA
1440831 GCAGCTGTCC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.56, C:0.14, G:0.11, T:0.19
Consensus pattern (36 bp):
AAAAAAAAATCAATATGGCAGCAAGAAACTCATCTA
Found at i:1441850 original size:17 final size:18
Alignment explanation
Indices: 1441828--1441866 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1441818 TTTCATTCTT
* *
1441828 AAAATATAAT-GAAGCCA
1 AAAATAAAATAGAAGACA
1441845 AAAATAAAATAGAAGACA
1 AAAATAAAATAGAAGACA
1441863 AAAA
1 AAAA
1441867 CCTAGTCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.69, C:0.08, G:0.10, T:0.13
Consensus pattern (18 bp):
AAAATAAAATAGAAGACA
Found at i:1442832 original size:21 final size:21
Alignment explanation
Indices: 1442812--1442860 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 21
1442802 AATATCTTTA
1442812 AAAAAATTTA-AATACT-ATTT
1 AAAAAATTTATAATA-TAATTT
*
1442832 AATAAATTTATAATATAATTTT
1 AAAAAATTTATAATATAA-TTT
1442854 AAAAAAT
1 AAAAAAT
1442861 ACTCTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 10 0.42
21 5 0.21
22 9 0.38
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAAAATTTATAATATAATTT
Found at i:1447896 original size:15 final size:16
Alignment explanation
Indices: 1447875--1447914 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
1447865 AAATAATTTA
*
1447875 ATATATTTTTAATATT
1 ATATATTTATAATATT
1447891 -TATA-TTATAATATT
1 ATATATTTATAATATT
1447905 ATATATTTAT
1 ATATATTTAT
1447915 TTTGTATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 9 0.43
15 8 0.38
16 4 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATATATTTATAATATT
Found at i:1447960 original size:20 final size:19
Alignment explanation
Indices: 1447923--1447962 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1447913 ATTTTGTATG
*
1447923 ATATAAATTATAAAAATAT
1 ATATAAATGATAAAAATAT
*
1447942 ATATAATATGATAATAATAT
1 ATATAA-ATGATAAAAATAT
1447962 A
1 A
1447963 AATTATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
ATATAAATGATAAAAATAT
Found at i:1447970 original size:20 final size:20
Alignment explanation
Indices: 1447932--1447970 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1447922 GATATAAATT
*
1447932 ATAAAAATATATATAATATG
1 ATAAAAATATAAATAATATG
* *
1447952 ATAATAATATAAATTATAT
1 ATAAAAATATAAATAATAT
1447971 ATTGAAAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
ATAAAAATATAAATAATATG
Done.