Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008955.1 Hibiscus syriacus cultivar Beakdansim tig00112285_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: 4658001
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 23
Found at i:1403354 original size:32 final size:31
Alignment explanation
Indices: 1403318--1403398 Score: 76
Period size: 31 Copynumber: 2.6 Consensus size: 31
1403308 GGAATACCTT
*
1403318 GGGGCCCGAGAGCCTACCCAAGAAAGTTAT-TC
1 GGGGCCCGAGAGCCTACCCAAG-AAG-GATCTC
* *
1403350 GGGGCCATG-GGGCCTACCCAAGAAGGATCTC
1 GGGGCC-CGAGAGCCTACCCAAGAAGGATCTC
* *
1403381 GAGGCCCCAGAGCCTACC
1 GGGGCCCGAGAGCCTACC
1403399 TAAGGGTCAT
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
30 2 0.05
31 18 0.46
32 18 0.46
33 1 0.03
ACGTcount: A:0.25, C:0.32, G:0.31, T:0.12
Consensus pattern (31 bp):
GGGGCCCGAGAGCCTACCCAAGAAGGATCTC
Found at i:1410255 original size:25 final size:25
Alignment explanation
Indices: 1410222--1410285 Score: 119
Period size: 25 Copynumber: 2.6 Consensus size: 25
1410212 AACTACATCT
*
1410222 CATGGACCAATTATATCCATTCATG
1 CATGTACCAATTATATCCATTCATG
1410247 CATGTACCAATTATATCCATTCATG
1 CATGTACCAATTATATCCATTCATG
1410272 CATGTACCAATTAT
1 CATGTACCAATTAT
1410286 CAATGTGTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.34
Consensus pattern (25 bp):
CATGTACCAATTATATCCATTCATG
Found at i:1413462 original size:17 final size:18
Alignment explanation
Indices: 1413430--1413464 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1413420 TTAAAATTAA
*
1413430 TGATTCACATTTTAAATT
1 TGATTCACAGTTTAAATT
1413448 TGATTCA-AGTTTAAATT
1 TGATTCACAGTTTAAATT
1413465 GTAAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.49
Consensus pattern (18 bp):
TGATTCACAGTTTAAATT
Found at i:1414463 original size:28 final size:28
Alignment explanation
Indices: 1414423--1414505 Score: 157
Period size: 28 Copynumber: 3.0 Consensus size: 28
1414413 AAAGTTTACA
1414423 AACATTCAAGTGGAATGTAATGTAGTTC
1 AACATTCAAGTGGAATGTAATGTAGTTC
1414451 AACATTCAAGTGGAATGTAATGTAGTTC
1 AACATTCAAGTGGAATGTAATGTAGTTC
*
1414479 AACATTTAAGTGGAATGTAATGTAGTT
1 AACATTCAAGTGGAATGTAATGTAGTT
1414506 TAAAAAAATC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 54 1.00
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (28 bp):
AACATTCAAGTGGAATGTAATGTAGTTC
Found at i:1419314 original size:27 final size:27
Alignment explanation
Indices: 1419276--1419338 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
1419266 TTGGATGATG
1419276 ATGTGCAACTGTATAGTGCTACTGACA
1 ATGTGCAACTGTATAGTGCTACTGACA
*
1419303 ATGTGCAACTGTATAGTGCTACTGGCA
1 ATGTGCAACTGTATAGTGCTACTGACA
1419330 ATGTGCAAC
1 ATGTGCAAC
1419339 AATGTACTAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (27 bp):
ATGTGCAACTGTATAGTGCTACTGACA
Found at i:1439905 original size:14 final size:14
Alignment explanation
Indices: 1439888--1439926 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
1439878 TAAGATTTTC
1439888 TTTTTGAAAAATCA
1 TTTTTGAAAAATCA
1439902 TTTTTGAAAAA-CA
1 TTTTTGAAAAATCA
* *
1439915 ATCTTGAAAAAT
1 TTTTTGAAAAAT
1439927 TACTCCCCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (14 bp):
TTTTTGAAAAATCA
Found at i:1440250 original size:23 final size:22
Alignment explanation
Indices: 1440210--1440253 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1440200 CCAAAATCAA
*
1440210 ATCCAAACATAAAAATCCAAAC
1 ATCCAAACACAAAAATCCAAAC
*
1440232 ATCCACAACACAAACATCCAAA
1 ATCCA-AACACAAAAATCCAAA
1440254 TTAGTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.57, C:0.32, G:0.00, T:0.11
Consensus pattern (22 bp):
ATCCAAACACAAAAATCCAAAC
Found at i:1440420 original size:21 final size:21
Alignment explanation
Indices: 1440382--1440421 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1440372 GAGTGTAAGT
*
1440382 GCATTGAGTCTGTCATTCATA
1 GCATTGAGTCTGTAATTCATA
1440403 GCATTGAGTC-GATAATTCA
1 GCATTGAGTCTG-TAATTCA
1440422 ATGTTTCGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (21 bp):
GCATTGAGTCTGTAATTCATA
Found at i:1442806 original size:21 final size:22
Alignment explanation
Indices: 1442758--1442810 Score: 90
Period size: 23 Copynumber: 2.4 Consensus size: 22
1442748 CCCTTTAGGG
1442758 GTATCGATACACATTCAAGGAAT
1 GTATCGATACACATTCAAGG-AT
1442781 GTATCGATACACATTCAAGG-T
1 GTATCGATACACATTCAAGGAT
1442802 GTATCGATA
1 GTATCGATA
1442811 TATAGCAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 10 0.33
23 20 0.67
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (22 bp):
GTATCGATACACATTCAAGGAT
Found at i:1442925 original size:549 final size:548
Alignment explanation
Indices: 1441888--1442992 Score: 1861
Period size: 549 Copynumber: 2.0 Consensus size: 548
1441878 CAAATGCTCG
*
1441888 ATATCTATTTCGAACTAGAACTAACTAAAACAAGTCATATGTTCAAAAATCAATAAAATAGTGTT
1 ATATCTATTTCGAACTAGAACTAACTAAAACAAGTCATATGTTAAAAAATCAATAAAATAGTGTT
*
1441953 TTGGAAAAATTACCTTGAAAATTTTGGATTTGAGTGGAATGTGTTGATGTTTGCACGATTTTGAT
66 TTAGAAAAATTACCTTGAAAATTTTGGATTTGAGTGGAATGTGTTGATGTTTGCACGATTTTGAT
1442018 GATCATAGCAGGATTTGAAGTTGAAAACTAGTTGAATTCCGACTTGAATTGAAGGTTTTGAGCAA
131 GATCATAGCAGGATTTGAAGTTGAAAACTAGTTGAATTCCGACTTGAATTGAAGGTTTTGAGCAA
* * * *
1442083 AATAAAGAGTAGGGTTGAGATAGGATAGAACGGCGGATAAGTGGTATATTTTGGGGTTTTGGCAA
196 AATAAAGAGTAGGGTTGAGAGAGGATAGAACGACAGATAAGTGATATATTTTGGGGTTTTGGCAA
1442148 AAATGAGTTTTTAGGGATTTAAAGCCTAAACCCGACAGAGGGTATAGATACCCCTCTAGAGGTAT
261 AAATGAGTTTTTAGGGATTTAAAGCCTAAACCCGACAGAGGGTATAGATACCCCTCTAGAGGTAT
* * ** *
1442213 CGATACACATTCAAGGAATATATCGGTACATATTCAAGGTGTATTTATATATAGCAAGGGGGTAT
326 CGATACACATTCAAGGAATATATCGATACACATTCAAGGTGTATCGATATATAGCAAAGGGGTAT
* * *
1442278 CAATACCTAGGTATTGATACACTTTGCACAAAAATGTCAAAATCTGTTTTTAAGCACTTATAATG
391 CAATACCTAGGTATCGATACACTTTGCACAAAAATATCAAAATATGTTTTTAAGCACTTATAATG
1442343 CTAAATTAATTAGCTCTAGTGGTATTGGCAACTCATATAACGAAAATTAACTATGTTCAATCAAT
456 CTAAATTAATTAGCTCTAGTGGTATTGGCAACTCATATAACGAAAATTAACTATGTTCAATCAAT
* *
1442408 TGAATCCACTCTTAAATTTTATTTAAAC
521 TAAATCCACTCTTAAAATTTATTTAAAC
* * * *
1442436 ATATCTATTTTGAACTAGAACTAACTAAAACTAGTCCTATGTTAAAAAATCAATAAAATTGTGTT
1 ATATCTATTTCGAACTAGAACTAACTAAAACAAGTCATATGTTAAAAAATCAATAAAATAGTGTT
1442501 TTAGAAAAATTACCTTGAAAATTTTGGATTTGAGTGGAATGTGTTGATGTTTGCACGATTTTGAT
66 TTAGAAAAATTACCTTGAAAATTTTGGATTTGAGTGGAATGTGTTGATGTTTGCACGATTTTGAT
* * *
1442566 GATCATAGCAGTATTTGAAGTTGAAAACTAGTTGAATTCTGATTTGAATTGAAGGTTTTGAGCAA
131 GATCATAGCAGGATTTGAAGTTGAAAACTAGTTGAATTCCGACTTGAATTGAAGGTTTTGAGCAA
* * * * *
1442631 AATAGAGAGTATGGGTTGAGAGAGGATAGAATGATAGATGAGTGATATGTTTTGGGGTTTTGGCA
196 AATAAAGAGTA-GGGTTGAGAGAGGATAGAACGACAGATAAGTGATATATTTTGGGGTTTTGGCA
* * * * *
1442696 AAAATGAGTTTTTAGGGATTTAAAGCCTAAACCCGACAGGGGGTATCGGTACCCCTTTAGGGGTA
260 AAAATGAGTTTTTAGGGATTTAAAGCCTAAACCCGACAGAGGGTATAGATACCCCTCTAGAGGTA
*
1442761 TCGATACACATTCAAGGAATGTATCGATACACATTCAAGGTGTATCGATATATAGCAAAGGGGTA
325 TCGATACACATTCAAGGAATATATCGATACACATTCAAGGTGTATCGATATATAGCAAAGGGGTA
*
1442826 TCGATACCTAGGTATCGATACACTTTGCACAAAAATATCAAAATATGTTTTTAAGCACTTATAAT
390 TCAATACCTAGGTATCGATACACTTTGCACAAAAATATCAAAATATGTTTTTAAGCACTTATAAT
*
1442891 GCTAAATTAATTAGCTCTAGTGGTATTGGCAACTCATATAATGAAAATTAACTATGTTCAATCAA
455 GCTAAATTAATTAGCTCTAGTGGTATTGGCAACTCATATAACGAAAATTAACTATGTTCAATCAA
*
1442956 TTAAATCCACTCTTAAAATTTATTTTAAC
520 TTAAATCCACTCTTAAAATTTATTTAAAC
1442985 ATAT-TATT
1 ATATCTATT
1442993 AATTTTCACT
Statistics
Matches: 519, Mismatches: 37, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
548 200 0.39
549 319 0.61
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (548 bp):
ATATCTATTTCGAACTAGAACTAACTAAAACAAGTCATATGTTAAAAAATCAATAAAATAGTGTT
TTAGAAAAATTACCTTGAAAATTTTGGATTTGAGTGGAATGTGTTGATGTTTGCACGATTTTGAT
GATCATAGCAGGATTTGAAGTTGAAAACTAGTTGAATTCCGACTTGAATTGAAGGTTTTGAGCAA
AATAAAGAGTAGGGTTGAGAGAGGATAGAACGACAGATAAGTGATATATTTTGGGGTTTTGGCAA
AAATGAGTTTTTAGGGATTTAAAGCCTAAACCCGACAGAGGGTATAGATACCCCTCTAGAGGTAT
CGATACACATTCAAGGAATATATCGATACACATTCAAGGTGTATCGATATATAGCAAAGGGGTAT
CAATACCTAGGTATCGATACACTTTGCACAAAAATATCAAAATATGTTTTTAAGCACTTATAATG
CTAAATTAATTAGCTCTAGTGGTATTGGCAACTCATATAACGAAAATTAACTATGTTCAATCAAT
TAAATCCACTCTTAAAATTTATTTAAAC
Found at i:1458795 original size:18 final size:18
Alignment explanation
Indices: 1458754--1458796 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1458744 AACTCCAACG
*
1458754 TTCTTCTTTTTCTCCGTC
1 TTCTTCTTTGTCTCCGTC
*
1458772 TCCTTCTTTGTCT-CGTCC
1 TTCTTCTTTGTCTCCGT-C
1458790 TTCTTCT
1 TTCTTCT
1458797 CAAGGTTTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.00, C:0.35, G:0.07, T:0.58
Consensus pattern (18 bp):
TTCTTCTTTGTCTCCGTC
Found at i:1466474 original size:32 final size:32
Alignment explanation
Indices: 1466397--1466610 Score: 189
Period size: 32 Copynumber: 6.7 Consensus size: 32
1466387 GTAACTACTA
** ** * *
1466397 TGCATTATCTGAATGTGACACTGGCACTGTTG
1 TGCATTATCTGAATGCAACACTAACAATATTG
* * * * *
1466429 TGCATTTTTTGAATACGACACTAACAATGTTG
1 TGCATTATCTGAATGCAACACTAACAATATTG
* * *
1466461 TGTATTATCTGAATGCAACAATAA-AACTATTT
1 TGCATTATCTGAATGCAACACTAACAA-TATTG
* *
1466493 TGCATTATCTGAATGCAACACTGACACTATTG
1 TGCATTATCTGAATGCAACACTAACAATATTG
* *
1466525 TACATTATCTGAATGCAACACTAACATTATTG
1 TGCATTATCTGAATGCAACACTAACAATATTG
* * * *
1466557 TGCATTATTTAAATGCAACAGTGAA-ACTATTG
1 TGCATTATCTGAATGCAACACT-AACAATATTG
*
1466589 TGCATTATCTGAATGTAACACT
1 TGCATTATCTGAATGCAACACT
1466611 CTGTTAGTAC
Statistics
Matches: 147, Mismatches: 32, Indels: 6
0.79 0.17 0.03
Matches are distributed among these distances:
31 2 0.01
32 142 0.97
33 3 0.02
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (32 bp):
TGCATTATCTGAATGCAACACTAACAATATTG
Found at i:1466538 original size:96 final size:96
Alignment explanation
Indices: 1466397--1466610 Score: 275
Period size: 96 Copynumber: 2.2 Consensus size: 96
1466387 GTAACTACTA
* * * * * * * *
1466397 TGCATTATCTGAATGTGACACTGGCACTGTTGTGCATTTTTTGAATACGACACTAACAATGTTGT
1 TGCATTATCTGAATGTAACACTGACACTATTGTACATTATCTGAATACAACACTAACAATATTGT
* * *
1466462 GTATTATCTGAATGCAACAATAAAACTATTT
66 GCATTATCTAAATGCAACAATAAAACTATTG
* * *
1466493 TGCATTATCTGAATGCAACACTGACACTATTGTACATTATCTGAATGCAACACTAACATTATTGT
1 TGCATTATCTGAATGTAACACTGACACTATTGTACATTATCTGAATACAACACTAACAATATTGT
* * *
1466558 GCATTATTTAAATGCAACAGTGAAACTATTG
66 GCATTATCTAAATGCAACAATAAAACTATTG
1466589 TGCATTATCTGAATGTAACACT
1 TGCATTATCTGAATGTAACACT
1466611 CTGTTAGTAC
Statistics
Matches: 100, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
96 100 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (96 bp):
TGCATTATCTGAATGTAACACTGACACTATTGTACATTATCTGAATACAACACTAACAATATTGT
GCATTATCTAAATGCAACAATAAAACTATTG
Found at i:1469963 original size:66 final size:63
Alignment explanation
Indices: 1469864--1469993 Score: 206
Period size: 66 Copynumber: 2.0 Consensus size: 63
1469854 CGATAGGGTC
* * *
1469864 ATATTTTTTAAAAAAATGGTCATGTTGGATATTTTAAGGTTTTACCCGAAGGGTGGAAGTTGA
1 ATATTTTTAAAAAAAATGGTCAGGTTGGATATTTTAAGGTTTAACCCGAAGGGTGGAAGTTGA
1469927 ATATTTTTAAAAATAAATTTGGTCAGGTTGGATATTTTAAGGTTTAACCCGAAGGGTGGAAGTTG
1 ATATTTTTAAAAA-AAA--TGGTCAGGTTGGATATTTTAAGGTTTAACCCGAAGGGTGGAAGTTG
1469992 A
63 A
1469993 A
1 A
1469994 AAAACTCTGA
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
63 12 0.20
64 3 0.05
66 46 0.75
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (63 bp):
ATATTTTTAAAAAAAATGGTCAGGTTGGATATTTTAAGGTTTAACCCGAAGGGTGGAAGTTGA
Found at i:1470798 original size:16 final size:16
Alignment explanation
Indices: 1470777--1470809 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1470767 TGCTGCCCTT
1470777 ATAATTTTTCAATTGC
1 ATAATTTTTCAATTGC
1470793 ATAATTTTTCAATTGC
1 ATAATTTTTCAATTGC
1470809 A
1 A
1470810 CCCTTATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.48
Consensus pattern (16 bp):
ATAATTTTTCAATTGC
Found at i:1482409 original size:15 final size:16
Alignment explanation
Indices: 1482377--1482410 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1482367 TAATTACATC
1482377 TAGAAACAATATAAAT
1 TAGAAACAATATAAAT
*
1482393 TAGAAACCATA-AAAT
1 TAGAAACAATATAAAT
1482408 TAG
1 TAG
1482411 CCTTGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.59, C:0.09, G:0.09, T:0.24
Consensus pattern (16 bp):
TAGAAACAATATAAAT
Found at i:1484425 original size:15 final size:16
Alignment explanation
Indices: 1484402--1484434 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1484392 TAATTTATAC
1484402 ATAAATTTT-AATTTT
1 ATAAATTTTAAATTTT
*
1484417 ATAACTTTTAAATTTT
1 ATAAATTTTAAATTTT
1484433 AT
1 AT
1484435 TTTTTATAAG
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:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
ATAAATTTTAAATTTT
Found at i:1486279 original size:6 final size:6
Alignment explanation
Indices: 1486268--1486302 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
1486258 ATGTTTTATA
1486268 TATGGC TATGGC TATGGC TATGGC TATGGC TATGG
1 TATGGC TATGGC TATGGC TATGGC TATGGC TATGG
1486303 AATGTGGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.14, G:0.34, T:0.34
Consensus pattern (6 bp):
TATGGC
Found at i:1490576 original size:2 final size:2
Alignment explanation
Indices: 1490569--1490603 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1490559 CATGAACAAG
1490569 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
1490604 GTAAATAAGA
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:1490723 original size:2 final size:2
Alignment explanation
Indices: 1490716--1490772 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
1490706 ACATACATAC
1490716 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
1490757 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
1490773 TTCGTTGTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1492048 original size:35 final size:36
Alignment explanation
Indices: 1492002--1492082 Score: 128
Period size: 35 Copynumber: 2.3 Consensus size: 36
1491992 AACACAATCA
* **
1492002 TCAATTACATTCTAAACCTCAAATT-CTAAAATGTT
1 TCAATTACATTCTAAACCTCAAATTCCAAAAATACT
1492037 TCAATTACATTCTAAACCTCAAATTCCAAAAATACT
1 TCAATTACATTCTAAACCTCAAATTCCAAAAATACT
1492073 TCAATTACAT
1 TCAATTACAT
1492083 GCCCAACCCC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 25 0.60
36 17 0.40
ACGTcount: A:0.42, C:0.22, G:0.01, T:0.35
Consensus pattern (36 bp):
TCAATTACATTCTAAACCTCAAATTCCAAAAATACT
Found at i:1493080 original size:35 final size:36
Alignment explanation
Indices: 1493011--1493091 Score: 110
Period size: 35 Copynumber: 2.3 Consensus size: 36
1493001 GGGGTTGGGC
*
1493011 ATATAATTGAAGTATTTTTGGAATTTGAAATTTAGA
1 ATATAATTGAAGCATTTTTGGAATTTGAAATTTAGA
* ***
1493047 ATATAATTGAAGCA-TTTTGGATTTTGGGGTTTAGA
1 ATATAATTGAAGCATTTTTGGAATTTGAAATTTAGA
1493082 ATATAATTGA
1 ATATAATTGA
1493092 TGACTATATT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 27 0.68
36 13 0.32
ACGTcount: A:0.36, C:0.01, G:0.20, T:0.43
Consensus pattern (36 bp):
ATATAATTGAAGCATTTTTGGAATTTGAAATTTAGA
Found at i:1498068 original size:17 final size:18
Alignment explanation
Indices: 1498046--1498080 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1498036 CGATATTGAT
1498046 TGAAGT-AGTATCGATAC
1 TGAAGTGAGTATCGATAC
*
1498063 TGAAGTGTGTATCGATAC
1 TGAAGTGAGTATCGATAC
1498081 CCAAAGGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.31
Consensus pattern (18 bp):
TGAAGTGAGTATCGATAC
Found at i:1499475 original size:6 final size:6
Alignment explanation
Indices: 1499466--1499510 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
1499456 TCTGTTTTTT
* * *
1499466 CTTCTG CTTCTG CTTTTT CTTCTG CTTCTG CTTTTG CTTCTG CTT
1 CTTCTG CTTCTG CTTCTG CTTCTG CTTCTG CTTCTG CTTCTG CTT
1499511 TATTTCTGGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.29, G:0.13, T:0.58
Consensus pattern (6 bp):
CTTCTG
Found at i:1499475 original size:18 final size:18
Alignment explanation
Indices: 1499449--1499510 Score: 97
Period size: 18 Copynumber: 3.4 Consensus size: 18
1499439 TGACTCTTCT
* *
1499449 TTCTTCTTCTGTTTTTTC
1 TTCTGCTTCTGCTTTTTC
1499467 TTCTGCTTCTGCTTTTTC
1 TTCTGCTTCTGCTTTTTC
*
1499485 TTCTGCTTCTGCTTTTGC
1 TTCTGCTTCTGCTTTTTC
1499503 TTCTGCTT
1 TTCTGCTT
1499511 TATTTCTGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.00, C:0.26, G:0.11, T:0.63
Consensus pattern (18 bp):
TTCTGCTTCTGCTTTTTC
Found at i:1499487 original size:12 final size:12
Alignment explanation
Indices: 1499454--1499511 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
1499444 CTTCTTTCTT
* *
1499454 CTTCTGTTTTTT
1 CTTCTGCTTTTG
*
1499466 CTTCTGCTTCTG
1 CTTCTGCTTTTG
* * *
1499478 CTTTTTCTTCTG
1 CTTCTGCTTTTG
1499490 CTTCTGCTTTTG
1 CTTCTGCTTTTG
1499502 CTTCTGCTTT
1 CTTCTGCTTT
1499512 ATTTCTGGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.00, C:0.26, G:0.12, T:0.62
Consensus pattern (12 bp):
CTTCTGCTTTTG
Found at i:1508180 original size:14 final size:15
Alignment explanation
Indices: 1508143--1508181 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
1508133 ACTCATTTCA
1508143 GAGAATTTGAGAATT
1 GAGAATTTGAGAATT
* *
1508158 TAGAGTTTG-GAATT
1 GAGAATTTGAGAATT
1508172 GAGAATTTGA
1 GAGAATTTGA
1508182 AAGATTGTGA
Statistics
Matches: 19, Mismatches: 4, Indels: 2
0.76 0.16 0.08
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.36, C:0.00, G:0.28, T:0.36
Consensus pattern (15 bp):
GAGAATTTGAGAATT
Found at i:1508880 original size:124 final size:126
Alignment explanation
Indices: 1508249--1508974 Score: 1147
Period size: 124 Copynumber: 5.9 Consensus size: 126
1508239 TAATCGGAGT
*
1508249 ACTATTCACATGAAGGCGCGTTCCC-GGGGGCGCCTT-CATTATTTCGTCAGAGAATATGTT-TT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGGCGCCTTCCATTATTTCGTCAGAGAATATGTTATC
1508311 ATTGCCCTATTATGTCACTCATGT-CCTC-GGACACTAGATATATCAGTACCTATTATTTC
66 ATTGCCCTATTATGTCACTCATGTCCCTCGGGACACTAGATATATCAGTACCTATTATTTC
*
1508370 ACTATTCACATGAAGGC-TGTTCCCGGGGGCGCGCCTTCCATTA-TTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGG-GCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
1508433 CATTGCCCTATTATGTCACTCATGTCCC-GGGGACACTAG--ATATCAG-ACCTA-TATTTC
65 CATTGCCCTATTATGTCACTCATGTCCCTCGGGACACTAGATATATCAGTACCTATTATTTC
*
1508490 ACTA-TCATATGAAGGCGCGTTCCC-GGGGG-GCCTTCCATTATTTCGTC-GAGAATA-G-T-TC
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGGCGCCTTCCATTATTTCGTCAGAGAATATGTTATC
*
1508548 ATTGCCCTATTATGTCACACATGTCCCTCGGGACACTAGATATATCAGTACCTATTATTTC
66 ATTGCCCTATTATGTCACTCATGTCCCTCGGGACACTAGATATATCAGTACCTATTATTTC
* *
1508609 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGTGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGG-GCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1508674 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
65 CATTGCCCTATTATGTCACTCATGTCCCTC-GGGACACTAGATATATCAGTACCTATTATTTC
*
1508737 ACTATTCATATGAA-G-GCGTTCCCGGGGGGCGCCTTCCATTATTTCGTCAGAG-ATATGTTATC
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGGCGCCTTCCATTATTTCGTCAGAGAATATGTTATC
*
1508799 ATTGCCCTATTATGTCACACATGTCCCT-GGGACACTAGATATATCAGTACCTATTATTTC
66 ATTGCCCTATTATGTCACTCATGTCCCTCGGGACACTAGATATATCAGTACCTATTATTTC
* *
1508859 ACTATTCATATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATC
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGGCGCCTTCCATTATTTCGTCAGAGAATATGTTATC
*
1508924 ATTGCCCTATTATGTCCCTCATGTCCCTCGAGGACACTAGATATATCAGTA
66 ATTGCCCTATTATGTCACTCATGTCCCTCG-GGACACTAGATATATCAGTA
1508975 AATCAGGTAA
Statistics
Matches: 561, Mismatches: 17, Indels: 48
0.90 0.03 0.08
Matches are distributed among these distances:
114 28 0.05
115 11 0.02
116 1 0.00
117 25 0.04
118 12 0.02
119 25 0.04
120 41 0.07
121 30 0.05
122 79 0.14
123 48 0.09
124 91 0.16
125 59 0.11
126 15 0.03
127 51 0.09
128 45 0.08
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (126 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGGCGCCTTCCATTATTTCGTCAGAGAATATGTTATC
ATTGCCCTATTATGTCACTCATGTCCCTCGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:1508952 original size:249 final size:249
Alignment explanation
Indices: 1508249--1508974 Score: 1189
Period size: 249 Copynumber: 3.0 Consensus size: 249
1508239 TAATCGGAGT
* *
1508249 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCCTT-CATTATTTCGTCAGAGAATATGTTTTAT
1 ACTATTCATATGAAGGCGCGTTCCCGGGGGCGCCTTCCATTATTTCGTCAGAG-ATATGTTTCAT
* *
1508313 TGCCCTATTATGTCACTCATGT-CCTCGGACACTAGATATATCAGTACCTATTATTTCACTATTC
65 TGCCCTATTATGTCACACATGTCCCTGGGACACTAGATATATCAGTACCTATTATTTCACTATTC
*
1508377 ACATGAAGGC-TGTTCCCGGGGGCGCGCCTTCCATTA-TTCGTCAGAGAATATGTTATCATTGCC
130 ACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCC
1508440 CTATTATGTCACTCATGT-CC-CGGGGACACTAG--ATATCAG-ACCTATATTTC
195 CTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATATTTC
1508490 ACTA-TCATATGAAGGCGCGTTCCCGGGGG-GCCTTCCATTATTTCGTC-GAGA-ATAG-TTCAT
1 ACTATTCATATGAAGGCGCGTTCCCGGGGGCGCCTTCCATTATTTCGTCAGAGATAT-GTTTCAT
1508550 TGCCCTATTATGTCACACATGTCCCTCGGGACACTAGATATATCAGTACCTATTATTTCACTATT
65 TGCCCTATTATGTCACACATGTCCCT-GGGACACTAGATATATCAGTACCTATTATTTCACTATT
* *
1508615 CACATGAAGGCGCGTTCCCGGGGGCGTGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGC
129 CACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGC
1508680 CCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
194 CCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTA-TATTTC
1508737 ACTATTCATATGAA-G-GCGTTCCCGGGGGGCGCCTTCCATTATTTCGTCAGAGATATGTTATCA
1 ACTATTCATATGAAGGCGCGTTCCC-GGGGGCGCCTTCCATTATTTCGTCAGAGATATGTT-TCA
1508800 TTGCCCTATTATGTCACACATGTCCCTGGGACACTAGATATATCAGTACCTATTATTTCACTATT
64 TTGCCCTATTATGTCACACATGTCCCTGGGACACTAGATATATCAGTACCTATTATTTCACTATT
*
1508865 CATATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGC
129 CACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGC
* *
1508929 CCTATTATGTCCCTCATGTCCCTCGAGGACACTAGATATATCAGTA
194 CCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
1508975 AATCAGGTAA
Statistics
Matches: 454, Mismatches: 12, Indels: 30
0.92 0.02 0.06
Matches are distributed among these distances:
237 27 0.06
238 5 0.01
239 56 0.12
240 60 0.13
241 48 0.11
242 2 0.00
243 12 0.03
245 7 0.02
246 13 0.03
247 16 0.04
248 27 0.06
249 92 0.20
250 59 0.13
251 30 0.07
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (249 bp):
ACTATTCATATGAAGGCGCGTTCCCGGGGGCGCCTTCCATTATTTCGTCAGAGATATGTTTCATT
GCCCTATTATGTCACACATGTCCCTGGGACACTAGATATATCAGTACCTATTATTTCACTATTCA
CATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCC
TATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATATTTC
Found at i:1509274 original size:33 final size:33
Alignment explanation
Indices: 1509232--1509330 Score: 126
Period size: 33 Copynumber: 3.0 Consensus size: 33
1509222 AAATTTAATG
* *
1509232 TTAATTTTGAATACTATAATTTATATTTTAAAT
1 TTAAATTTGAATAATATAATTTATATTTTAAAT
* * * *
1509265 TTAAATTTGAATAATATTATTTTTATTTTTATT
1 TTAAATTTGAATAATATAATTTATATTTTAAAT
*
1509298 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTT-GAATAATATAATTTATATTTTAAA
1509331 AACATTTATC
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 35 0.64
34 20 0.36
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (33 bp):
TTAAATTTGAATAATATAATTTATATTTTAAAT
Found at i:1509883 original size:21 final size:21
Alignment explanation
Indices: 1509857--1509936 Score: 117
Period size: 21 Copynumber: 3.8 Consensus size: 21
1509847 AAAACCCTGC
*
1509857 GGCTAGGCATGTAACCTGGCG
1 GGCTAGGAATGTAACCTGGCG
*
1509878 GGCTAGGCATGTAACCTGGCG
1 GGCTAGGAATGTAACCTGGCG
1509899 GGCTAGGAATGTAACCCT-GCG
1 GGCTAGGAATGTAA-CCTGGCG
*
1509920 GGCTCGGAATGTAACCT
1 GGCTAGGAATGTAACCT
1509937 TGGAGATGGC
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.05
21 50 0.89
22 3 0.05
ACGTcount: A:0.21, C:0.24, G:0.35, T:0.20
Consensus pattern (21 bp):
GGCTAGGAATGTAACCTGGCG
Found at i:1511757 original size:34 final size:31
Alignment explanation
Indices: 1511714--1511802 Score: 97
Period size: 34 Copynumber: 2.7 Consensus size: 31
1511704 TTAATAATTC
*
1511714 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTATATAAATA-TA--TTAA
* *
1511748 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTATATAAATATATTAA
* *
1511779 TATAAAAAATAATAACTATTTAAA
1 TA-AAAAAATAATAATTATATAAA
1511803 AAAATACTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 6 0.13
32 17 0.36
33 2 0.04
34 22 0.47
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAAAAAATAATAATTATATAAATATATTAA
Found at i:1511759 original size:31 final size:33
Alignment explanation
Indices: 1511717--1511791 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 33
1511707 ATAATTCTAA
* * *
1511717 ATAAATAATAATTATATAAAT-ATTATTTTAAT
1 ATAAAAAATAATTATATAAATAAATATATTAAT
* *
1511749 A-AAAAAATAA-TATTTACATAAATATATTAAT
1 ATAAAAAATAATTATATAAATAAATATATTAAT
1511780 ATAAAAAATAAT
1 ATAAAAAATAAT
1511792 AACTATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
30 7 0.20
31 18 0.51
32 10 0.29
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
ATAAAAAATAATTATATAAATAAATATATTAAT
Found at i:1516254 original size:15 final size:15
Alignment explanation
Indices: 1516234--1516263 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1516224 CTTTCTTATA
1516234 GTTGTTGTTGGAATT
1 GTTGTTGTTGGAATT
*
1516249 GTTGTTGTTGTAATT
1 GTTGTTGTTGGAATT
1516264 CCAGCCTCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.30, T:0.57
Consensus pattern (15 bp):
GTTGTTGTTGGAATT
Found at i:1518926 original size:2 final size:2
Alignment explanation
Indices: 1518882--1518917 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
1518872 ATATAACAAC
*
1518882 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TCA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA T
1518918 CACATATATC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1526839 original size:23 final size:23
Alignment explanation
Indices: 1526809--1526871 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
1526799 CTGAATGATT
* *
1526809 CAGTGCTGACTGATTCATCAAAA
1 CAGTGCTGAATGATTCAACAAAA
1526832 CAGTGCTGAATGATTCAACAAAA
1 CAGTGCTGAATGATTCAACAAAA
1526855 CAGTGCTGAATGATTCA
1 CAGTGCTGAATGATTCA
1526872 GTACATAAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (23 bp):
CAGTGCTGAATGATTCAACAAAA
Found at i:1526972 original size:16 final size:16
Alignment explanation
Indices: 1526951--1526995 Score: 90
Period size: 16 Copynumber: 2.8 Consensus size: 16
1526941 ACAGAGCCTC
1526951 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
1526967 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
1526983 TGAATCATTCAGC
1 TGAATCATTCAGC
1526996 GCTTAATCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (16 bp):
TGAATCATTCAGCATT
Found at i:1527213 original size:22 final size:20
Alignment explanation
Indices: 1527169--1527213 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
1527159 TGGAATTATT
*
1527169 ATAATATTTTAAAATTAATA
1 ATAATATTTTAAAATAAATA
*
1527189 ATAATTTTTTATATAATAAATA
1 ATAATATTTTA-A-AATAAATA
1527211 ATA
1 ATA
1527214 TTAATTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.48
21 1 0.05
22 10 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATAATATTTTAAAATAAATA
Found at i:1527225 original size:22 final size:22
Alignment explanation
Indices: 1527200--1527242 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1527190 TAATTTTTTA
1527200 TATAATAAATAA-TATTAATTAT
1 TATAATAAATAATTA-TAATTAT
* *
1527222 TATATTTAATAATTATAATTA
1 TATAATAAATAATTATAATTA
1527243 ATCATTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TATAATAAATAATTATAATTAT
Found at i:1530689 original size:139 final size:139
Alignment explanation
Indices: 1530439--1531071 Score: 890
Period size: 139 Copynumber: 4.6 Consensus size: 139
1530429 CACTTGAATA
* * *
1530439 CGCG-TTCTCGGGGGCGCGTCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAATATA
1 CGCGTTTCT-GGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATG
*
1530503 TCACTCATGTCCCTCGGGGGCACTATTCATATCAGTACCTATTATGTTTGAGGGGACTTGGCAAA
65 TCACTCATGTCCCTCGGGGGCACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTGGCAAA
1530568 GTGGTGAAAG
130 GTGGTGAAAG
* * * * *
1530578 CGCGTTTCTGGGGGCACGTCTTCCATTATTTTGTTAGAGAACATGTTATCATTGTCCTATTATGT
1 CGCGTTTCTGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGT
*
1530643 CACTCATGTCCCTCGGGGGCACTATTCATGTCAGTACCTATTATGTTTGAGGAGACTTGGCAAAG
66 CACTCATGTCCCTCGGGGGCACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTGGCAAAG
*
1530708 TGGTGAAAA
131 TGGTGAAAG
* * * * * *
1530717 CGCATTTCCGGGGGCACGCCTTTCATTATTTTGTCAGAAAATATGTTATCATTACCCTATTATGT
1 CGCGTTTCTGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGT
*
1530782 CACTCATGTCTCTCGGGGGCACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTGGCAAAG
66 CACTCATGTCCCTCGGGGGCACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTGGCAAAG
1530847 TGGTGAAAG
131 TGGTGAAAG
* * *** * *
1530856 TGCGCTTCCAAGGGCGTGCCTTCCATTATTTTGTTAGAGAATATGTTATCATTGCCCTATTATGT
1 CGCGTTTCTGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGT
* * * **
1530921 CACTCATGTCCCTCGGGGGCACTATTCATGTCAGTACCTACTATGTTTGATGTGACTTAACAAAG
66 CACTCATGTCCCTCGGGGGCACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTGGCAAAG
1530986 TGGTGAAAG
131 TGGTGAAAG
* * * * * * * *
1530995 CGCGTTCCTGGGGGCGCGCCTTCGATTGTTATGCCAAAGAATATGTTATAATTGCCTTATTATGT
1 CGCGTTTCTGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGT
* *
1531060 GAGTCATGTCCC
66 CACTCATGTCCC
1531072 CGGAGACGCA
Statistics
Matches: 438, Mismatches: 55, Indels: 2
0.88 0.11 0.00
Matches are distributed among these distances:
139 434 0.99
140 4 0.01
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (139 bp):
CGCGTTTCTGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGT
CACTCATGTCCCTCGGGGGCACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTGGCAAAG
TGGTGAAAG
Found at i:1532111 original size:22 final size:20
Alignment explanation
Indices: 1532069--1532138 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 20
1532059 GTCATAAAAC
* *
1532069 CCTGCAGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
1532089 CCTGGCGGGCTAAGGAATGTAA
1 CCT-GCGGGCT-AGGAATGTAA
1532111 CCCTGCGGGCTAGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
1532132 CCCTGCG
1 -CCTGCG
1532139 AATATGGCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
20 3 0.07
21 23 0.51
22 16 0.36
23 3 0.07
ACGTcount: A:0.23, C:0.26, G:0.33, T:0.19
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:1532186 original size:42 final size:42
Alignment explanation
Indices: 1532131--1532220 Score: 103
Period size: 42 Copynumber: 2.2 Consensus size: 42
1532121 TAGGAATGTA
* *
1532131 ACCC-TGCGAATATGGCATATGAA-CTGGTGGGCTTGGCATAT
1 ACCCTTGCGAATATGGCATAT-AAGCTGGAGGGCTGGGCATAT
* * * *
1532172 ACCCTTGCGGATATGGTATCTAAGCTGGAGGGCTGGGCATGT
1 ACCCTTGCGAATATGGCATATAAGCTGGAGGGCTGGGCATAT
1532214 ACCCTTG
1 ACCCTTG
1532221 TAGCATCATC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
41 6 0.15
42 35 0.85
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.27
Consensus pattern (42 bp):
ACCCTTGCGAATATGGCATATAAGCTGGAGGGCTGGGCATAT
Found at i:1533968 original size:15 final size:15
Alignment explanation
Indices: 1533923--1534001 Score: 56
Period size: 15 Copynumber: 5.3 Consensus size: 15
1533913 TAATTAGCAC
1533923 AAATAATAATTA-AT
1 AAATAATAATTATAT
* * *
1533937 TAATAA-ATTTAAAAT
1 AAATAATAATT-ATAT
1533952 AAATAATAATTATAT
1 AAATAATAATTATAT
* * *
1533967 AAAT-ATTATTTTAAA
1 AAATAATAATTAT-AT
*
1533982 AAATAATATTTATAT
1 AAATAATAATTATAT
1533997 AAATA
1 AAATA
1534002 TAAAAATAAA
Statistics
Matches: 48, Mismatches: 12, Indels: 9
0.70 0.17 0.13
Matches are distributed among these distances:
13 3 0.06
14 12 0.25
15 25 0.52
16 8 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATAATAATTATAT
Found at i:1533988 original size:30 final size:31
Alignment explanation
Indices: 1533923--1534004 Score: 107
Period size: 30 Copynumber: 2.7 Consensus size: 31
1533913 TAATTAGCAC
*
1533923 AAATAATAATTA-ATTAATA-AATTTAAAAT
1 AAATAATAATTATATAAATATAATTTAAAAT
* *
1533952 AAATAATAATTATATAAATATTATTTTAAA-
1 AAATAATAATTATATAAATATAATTTAAAAT
*
1533982 AAATAATATTTATATAAATATAA
1 AAATAATAATTATATAAATATAA
1534005 AAATAAAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 12 0.26
30 27 0.59
31 7 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (31 bp):
AAATAATAATTATATAAATATAATTTAAAAT
Found at i:1534012 original size:30 final size:30
Alignment explanation
Indices: 1533952--1534016 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
1533942 AATTTAAAAT
* ***
1533952 AAATAATAATTATATAAATATTATTTTAAA
1 AAATAATAATTATATAAATATAAAAATAAA
*
1533982 AAATAATATTTATATAAATATAAAAATAAA
1 AAATAATAATTATATAAATATAAAAATAAA
1534012 AAATA
1 AAATA
1534017 TAACAACTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (30 bp):
AAATAATAATTATATAAATATAAAAATAAA
Found at i:1544999 original size:3 final size:3
Alignment explanation
Indices: 1544991--1545019 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1544981 AATTCAACTC
1544991 TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1545020 TGGATGAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:1548671 original size:21 final size:21
Alignment explanation
Indices: 1548642--1548703 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
1548632 ATCTAGAAAA
*
1548642 AAATTAATTAAATAAAATATT
1 AAATAAATTAAATAAAATATT
1548663 AAATAAATTAAATACAAAATATT
1 AAATAAATTAAAT--AAAATATT
1548686 -AA-AAA-TATAATAAAATAT
1 AAATAAATTA-AATAAAATAT
1548704 ACCTTAGACA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
19 7 0.19
20 2 0.05
21 18 0.49
22 2 0.05
23 8 0.22
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
AAATAAATTAAATAAAATATT
Found at i:1548743 original size:10 final size:10
Alignment explanation
Indices: 1548730--1548758 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1548720 ATAAGAGTAT
1548730 TTGAGAGAAG
1 TTGAGAGAAG
1548740 TTGAGAGAAG
1 TTGAGAGAAG
1548750 TTGAGAGAA
1 TTGAGAGAA
1548759 TTTGGTGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.38, T:0.21
Consensus pattern (10 bp):
TTGAGAGAAG
Found at i:1549812 original size:18 final size:18
Alignment explanation
Indices: 1549789--1549851 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
1549779 TAAATTTCAA
1549789 TAAAAAAGAATGTAAAGC
1 TAAAAAAGAATGTAAAGC
* *
1549807 TAAAAAA-TAT-TAAAATTC
1 TAAAAAAGAATGT-AAA-GC
1549825 AATAAAAAAGAATGTAAAGC
1 --TAAAAAAGAATGTAAAGC
1549845 TAAAAAA
1 TAAAAAA
1549852 TATCACCTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
16 1 0.03
17 5 0.14
18 15 0.43
20 8 0.23
21 5 0.14
22 1 0.03
ACGTcount: A:0.65, C:0.05, G:0.10, T:0.21
Consensus pattern (18 bp):
TAAAAAAGAATGTAAAGC
Found at i:1549851 original size:38 final size:38
Alignment explanation
Indices: 1549779--1549854 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
1549769 TAAAAGTGAA
*
1549779 TAAATTTCAATAAAAAAGAATGTAAAGCTAAAAAATAT
1 TAAAATTCAATAAAAAAGAATGTAAAGCTAAAAAATAT
1549817 TAAAATTCAATAAAAAAGAATGTAAAGCTAAAAAATAT
1 TAAAATTCAATAAAAAAGAATGTAAAGCTAAAAAATAT
1549855 CACCTATTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.25
Consensus pattern (38 bp):
TAAAATTCAATAAAAAAGAATGTAAAGCTAAAAAATAT
Found at i:1549953 original size:29 final size:30
Alignment explanation
Indices: 1549902--1549963 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
1549892 TAAAAAATAT
1549902 AAAATAAATATAAAATTACAATT-TTATTA
1 AAAATAAATATAAAATTACAATTGTTATTA
* * *
1549931 AAAATAAATA-AACATTATTAATTGTTGTTA
1 AAAATAAATATAAAATTA-CAATTGTTATTA
1549961 AAA
1 AAA
1549964 GTAATAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 6 0.21
29 14 0.50
30 8 0.29
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.37
Consensus pattern (30 bp):
AAAATAAATATAAAATTACAATTGTTATTA
Found at i:1550612 original size:179 final size:179
Alignment explanation
Indices: 1550363--1550725 Score: 577
Period size: 182 Copynumber: 2.0 Consensus size: 179
1550353 TATTTTAATA
*
1550363 TTTTTTATATTTTAAAAAAATTAATTTTAAAAGTCAATAAATTTTTCAAATATATATGAAATTTA
1 TTTTTTATATTTTAAAAAAATTAATTTTAAAAGTCAATAAATTTTTCAAAAATATATGAAATTTA
* *
1550428 TAATTTTTTAAATTATAAAATA-T-TTATCATCTTCATCATCATTTTGTAAAATAAATACTAGTT
66 TAATTTTTTAAATTATAAAATATTATTATCATCATCATCATCATTTTGTAAAAGAAATACTAGTT
* * *
1550491 ATAAAACTTTTATAAAATTATTCATATTTTAAAATACTTACCCTTAAAT
131 ATAAAAATTTTATAAAATTATTCATATTTTAAAATACTTACCCTCAAAG
* * * **
1550540 TTTTTTATATTTTTAAACAATTAATTTTAAAAGTTAATATTTTTTTTTCAAAAATATATGAAATT
1 TTTTTTATATTTTAAAAAAATTAATTTTAAAAGTCAATA--AATTTTTCAAAAATATATGAAATT
*
1550605 TATAATTTTTTAAATTATAAAATATTTATTATTATCATCATCATCATTTTGTAAAAGAAATACTA
64 TATAATTTTTTAAATTATAAAATA-TTATTATCATCATCATCATCATTTTGTAAAAGAAATACTA
1550670 GTTATAAAAATTTTATAAAATTATTCATATTTTAAAATACTTACCCTCAAAG
128 GTTATAAAAATTTTATAAAATTATTCATATTTTAAAATACTTACCCTCAAAG
1550722 TTTT
1 TTTT
1550726 CCTATACTAT
Statistics
Matches: 169, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
177 36 0.21
179 45 0.27
181 1 0.01
182 87 0.51
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.47
Consensus pattern (179 bp):
TTTTTTATATTTTAAAAAAATTAATTTTAAAAGTCAATAAATTTTTCAAAAATATATGAAATTTA
TAATTTTTTAAATTATAAAATATTATTATCATCATCATCATCATTTTGTAAAAGAAATACTAGTT
ATAAAAATTTTATAAAATTATTCATATTTTAAAATACTTACCCTCAAAG
Found at i:1550699 original size:518 final size:513
Alignment explanation
Indices: 1550029--1551061 Score: 1764
Period size: 518 Copynumber: 2.0 Consensus size: 513
1550019 ATTTAAAATA
*
1550029 TTTTATATTTTTAAACAATTAATTTAAAAGTTAATAATATTTTTCAAATATATATGAAATTTATA
1 TTTTATATTTTTAAACAATTAATTTAAAAGTTAATAATATTTTTCAAAAATATATGAAATTTATA
1550094 ATTTTTTAAATTATAAAATATTTATCATCATCATCATCATTTTGTAAAAGAAATACTAGTTATAA
66 ATTTTTTAAATTATAAAATATTTATCATCATCATCATCATTTTGTAAAAGAAATACTAGTTATAA
*
1550159 AACTTTTATAAAATTATTCATATTTTAAAATACATACCCTCAAAACTTTCCTATACTATATTATA
131 AAATTTTATAAAATTATTCATATTTTAAAATACATACCCTCAAAACTTTCCTATACTATATTATA
1550224 CA-TATTGTGTAATCTCATGCAAAAATCAAAATAATTTTATTAAAAATAAATAAACATTATTAAC
196 -AGTATTGTGTAATCTCATGCAAAAATCAAAATAATTTTATTAAAAATAAATAAACATTATTAAC
* * *
1550288 TGTTGTT-AAAAAATAATAAATAATGAATAATAATTTATTTGATACCTCAAATGTAATTAAAATT
260 TGTT-TTAAAAAAATAATAAATAATGAATAATAATTCATTTGATACCTCAAATATAATTAAAAAT
* *
1550352 TTATTTTAATATTTTTTATATTTTAAAAAAATTAATTTTAAAAGTCAATAAATTTTTCAAATATA
324 TTATTTTAATATTTTTTATATTTTAAAAAAATTAATTTTAAAAGTCAATAAAATTTTCAAAAATA
*
1550417 TATGAAATTTATAATTTTTTAAATTATAAAATATTTATCATCTTCATCATCATTTTGTAAAATAA
389 TATGAAATTTATAATTTTTTAAATTATAAAATATTTATCATCATCATCATCATTTTGTAAAATAA
*
1550482 ATACTAGTTATAAAACTTTTATAAAATTATTCATATTTTAAAATACTTACCCTTAAATTT
454 ATACTAGTTATAAAACTTTTATAAAATTATTCATATTTTAAAATACTTACCCTTAAAGTT
* *
1550542 TTTTATATTTTTAAACAATTAATTTTAAAAGTTAATATTTTTTTTTCAAAAATATATGAAATTTA
1 TTTTATATTTTTAAACAATTAA-TTTAAAAGTTAATA-ATATTTTTCAAAAATATATGAAATTTA
*
1550607 TAATTTTTTAAATTATAAAATATTTATTATTATCATCATCATCATTTTGTAAAAGAAATACTAGT
64 TAATTTTTTAAATTATAAAATA--T-TTATCATCATCATCATCATTTTGTAAAAGAAATACTAGT
* **
1550672 TATAAAAATTTTATAAAATTATTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTATA
126 TATAAAAATTTTATAAAATTATTCATATTTTAAAATACATACCCTCAAAACTTTCCTATACTATA
* *
1550737 TTATAAGTATTGTGTAATTTCATGCAAAAATTAAAATAATTTTATTAAAAATAAATAAACATTAT
191 TTATAAGTATTGTGTAATCTCATGCAAAAATCAAAATAATTTTATTAAAAATAAATAAACATTAT
* * *
1550802 TAACTGTTTTAAAAAAATAATAATTAATGAATAATAATTCATTTGATCCCTTAAATATAATTAAA
256 TAACTGTTTTAAAAAAATAATAAATAATGAATAATAATTCATTTGATACCTCAAATATAATTAAA
* *
1550867 AATTTATTTTAATATTTTTTATATTTTTAAACAATTAATTTTAAAAGTCAATAAAATTTTCAAAA
321 AATTTATTTTAATATTTTTTATATTTTAAAAAAATTAATTTTAAAAGTCAATAAAATTTTCAAAA
* *
1550932 ATATATGAAATTTATAATTTTTTAATTTATAAAATATTTATCATCATCATTATCATTTTGTAAAA
386 ATATATGAAATTTATAATTTTTTAAATTATAAAATATTTATCATCATCATCATCATTTTGTAAAA
*
1550997 TAAATACTAGTTATAAAACTTTTATAAAATTATTCATATTTTAAAATACTTACCTTTAAAGTT
451 TAAATACTAGTTATAAAACTTTTATAAAATTATTCATATTTTAAAATACTTACCCTTAAAGTT
1551060 TT
1 TT
1551062 CCTATACTAG
Statistics
Matches: 488, Mismatches: 25, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
513 22 0.05
514 14 0.03
515 46 0.09
517 4 0.01
518 402 0.82
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (513 bp):
TTTTATATTTTTAAACAATTAATTTAAAAGTTAATAATATTTTTCAAAAATATATGAAATTTATA
ATTTTTTAAATTATAAAATATTTATCATCATCATCATCATTTTGTAAAAGAAATACTAGTTATAA
AAATTTTATAAAATTATTCATATTTTAAAATACATACCCTCAAAACTTTCCTATACTATATTATA
AGTATTGTGTAATCTCATGCAAAAATCAAAATAATTTTATTAAAAATAAATAAACATTATTAACT
GTTTTAAAAAAATAATAAATAATGAATAATAATTCATTTGATACCTCAAATATAATTAAAAATTT
ATTTTAATATTTTTTATATTTTAAAAAAATTAATTTTAAAAGTCAATAAAATTTTCAAAAATATA
TGAAATTTATAATTTTTTAAATTATAAAATATTTATCATCATCATCATCATTTTGTAAAATAAAT
ACTAGTTATAAAACTTTTATAAAATTATTCATATTTTAAAATACTTACCCTTAAAGTT
Found at i:1551758 original size:16 final size:16
Alignment explanation
Indices: 1551739--1551786 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1551729 TAAGTTATTA
1551739 GTTAAAATTTAGATCG
1 GTTAAAATTTAGATCG
** *
1551755 GTTAAATAAGT-GATCA
1 GTTAAA-ATTTAGATCG
1551771 GTTAAAATTTAGATCG
1 GTTAAAATTTAGATCG
1551787 TTTATGTTAT
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
15 2 0.08
16 20 0.83
17 2 0.08
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (16 bp):
GTTAAAATTTAGATCG
Found at i:1551760 original size:32 final size:32
Alignment explanation
Indices: 1551718--1551786 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
1551708 AAAATGATGT
* * *
1551718 GATCAGTTAAATAAGTTATTAGTTAAAATTTA
1 GATCGGTTAAATAAGTGATCAGTTAAAATTTA
1551750 GATCGGTTAAATAAGTGATCAGTTAAAATTTA
1 GATCGGTTAAATAAGTGATCAGTTAAAATTTA
1551782 GATCG
1 GATCG
1551787 TTTATGTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.36
Consensus pattern (32 bp):
GATCGGTTAAATAAGTGATCAGTTAAAATTTA
Found at i:1551877 original size:64 final size:64
Alignment explanation
Indices: 1551799--1551918 Score: 204
Period size: 64 Copynumber: 1.9 Consensus size: 64
1551789 TATGTTATAT
* *
1551799 CATTTAATAAAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATAAAATAAA
1 CATTTAATAAAAAATATTATCAAGTACAATAACATATTAAGTAACGCTTATATAATAAAATAAA
**
1551863 CATTTAATCGAAAATATTATCAAGTACAATAACATATTAAGTAACGCTTATATAAT
1 CATTTAATAAAAAATATTATCAAGTACAATAACATATTAAGTAACGCTTATATAAT
1551919 GTAATAGGTA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 52 1.00
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (64 bp):
CATTTAATAAAAAATATTATCAAGTACAATAACATATTAAGTAACGCTTATATAATAAAATAAA
Found at i:1552323 original size:199 final size:195
Alignment explanation
Indices: 1551956--1552643 Score: 746
Period size: 199 Copynumber: 3.5 Consensus size: 195
1551946 TTTTATAAGT
* * * *
1551956 AAACCGGTATATTTATACCGGTAACATTGCAAATTTACCTATTATATTATAATTATCGGTTTCGA
1 AAACCGGTATATTTATACAGGT-ACATTGTAAATTTACATATTACATTATAATTATCGGTTTCGA
* * * *
1552021 TGTTTTTTGGATAGATACAATTT--GAAATGTATCGACACTTTATGTGTGCACCTCATTGGACAT
65 T-TTTTTGGGATAGATAC-TTTTAATAAATGTATCGACACTTTATGTGTGCACC-CTTTGG-CAT
* * * * *
1552084 TTATTATGGAAAAAAGTATCGACACAAACTTAAAAAGTGTCGATACATTAT-TTAGACATATTTT
126 TCATTATGGACAAAAGTATCGACACAAATTTAACAAGTGTCGATACATTATGTT-GACCTATTTT
1552148 CTCATA
190 CTCATA
* * * *
1552154 AAACCGGTATATTTCTATCAGGTACATTGTAAATTTACATATCACGTTGTAATTATCGGTTTCGA
1 AAACCGGTATATTTATA-CAGGTACATTGTAAATTTACATATTACATTATAATTATCGGTTTCGA
* *
1552219 TATTTTTGGGATCGATACTTTTAATAAATGTATCGATACTTTATGTGTGCACCCGTTTGGCATTC
65 T-TTTTTGGGATAGATACTTTTAATAAATGTATCGACACTTTATGTGTGCACCC-TTTGGCATTC
* * *
1552284 ATTATGGACAAAATGTATCGACACAAATTTAACAAGTGTCAATACTTTATGCTGACCTATTTTCT
128 ATTATGGACAAAA-GTATCGACACAAATTTAACAAGTGTCGATACATTATGTTGACCTATTTTCT
1552349 CATA
192 CATA
*
1552353 AAACCGGTATA-TT-T--A--T--ATTGTAAATTTACATATTACATTATAATTATCGATTTCGAT
1 AAACCGGTATATTTATACAGGTACATTGTAAATTTACATATTACATTATAATTATCGGTTTCGAT
* * *
1552410 TTTATTGGGATAAATACTTTTAATAAATGTATCGACACTTTATGTGTGCATCTCATTTGGGTATT
66 TTT-TTGGGATAGATACTTTTAATAAATGTATCGACACTTTATGTGTGCA-C-CCTTT-GGCATT
* ** *
1552475 CATTTTGGACAATAAGTATCGACACAAATTCCACAA--GT-G-TACATTATGTTGACCTGTTTTC
127 CATTATGGACAA-AAGTATCGACACAAATTTAACAAGTGTCGATACATTATGTTGACCTATTTTC
*
1552536 TAAT-
191 TCATA
* * * * *
1552540 TAACCGGTATATTTATACCGGTTACATTGTTAATTTACCTATTACATTATAATTATTGGTTTCGA
1 AAACCGGTATATTTATACAGG-TACATTGTAAATTTACATATTACATTATAATTATCGGTTTCGA
*
1552605 TGTTTTTTGGG-TCGATACTTTTAGA-AAATGTATCGACAC
65 --TTTTTTGGGATAGATACTTTTA-ATAAATGTATCGACAC
1552644 ATATTTAGGT
Statistics
Matches: 419, Mismatches: 48, Indels: 48
0.81 0.09 0.09
Matches are distributed among these distances:
187 10 0.02
188 24 0.06
189 4 0.01
190 82 0.20
191 4 0.01
192 37 0.09
193 2 0.00
194 2 0.00
196 60 0.14
197 10 0.02
198 90 0.21
199 93 0.22
200 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (195 bp):
AAACCGGTATATTTATACAGGTACATTGTAAATTTACATATTACATTATAATTATCGGTTTCGAT
TTTTTGGGATAGATACTTTTAATAAATGTATCGACACTTTATGTGTGCACCCTTTGGCATTCATT
ATGGACAAAAGTATCGACACAAATTTAACAAGTGTCGATACATTATGTTGACCTATTTTCTCATA
Found at i:1553521 original size:10 final size:10
Alignment explanation
Indices: 1553508--1553621 Score: 84
Period size: 10 Copynumber: 10.3 Consensus size: 10
1553498 GATGTTTATG
1553508 TATGTTCGTT
1 TATGTTCGTT
*
1553518 TATGTTCATTTAT
1 TATGTTC--GT-T
1553531 TATGTTCGTT
1 TATGTTCGTT
1553541 TATGTTCGTTT
1 TATGTTCG-TT
*
1553552 GTTTGAGTTCGTT
1 -TAT--GTTCGTT
*
1553565 TACGTTCGTT
1 TATGTTCGTT
1553575 TATGTTCGTTTGTT
1 TATGTTC----GTT
*
1553589 TGTGTTCGTT
1 TATGTTCGTT
*
1553599 TACGTTCGTT
1 TATGTTCGTT
1553609 TATGTTCGTT
1 TATGTTCGTT
1553619 TAT
1 TAT
1553622 CATTTAAATG
Statistics
Matches: 83, Mismatches: 10, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
10 52 0.63
11 3 0.04
12 4 0.05
13 10 0.12
14 14 0.17
ACGTcount: A:0.11, C:0.11, G:0.20, T:0.59
Consensus pattern (10 bp):
TATGTTCGTT
Found at i:1553529 original size:24 final size:24
Alignment explanation
Indices: 1553501--1553621 Score: 112
Period size: 24 Copynumber: 5.2 Consensus size: 24
1553491 CATACTCGAT
1553501 GTTTATGTATGTTCGTTTATGTTC
1 GTTTATGTATGTTCGTTTATGTTC
*
1553525 ATTTAT-TATGTTCGTTTATGTTC
1 GTTTATGTATGTTCGTTTATGTTC
* * *
1553548 GTTTGTTTGA-GTTCGTTTACGTTC
1 GTTTATGT-ATGTTCGTTTATGTTC
* *
1553572 GTTTATGT-TCGTTTGTTTGTGTTC
1 GTTTATGTAT-GTTCGTTTATGTTC
*
1553596 G--T-T-TACGTTCGTTTATGTTC
1 GTTTATGTATGTTCGTTTATGTTC
1553616 GTTTAT
1 GTTTAT
1553622 CATTTAAATG
Statistics
Matches: 77, Mismatches: 12, Indels: 17
0.73 0.11 0.16
Matches are distributed among these distances:
20 14 0.18
21 1 0.01
22 2 0.03
23 22 0.29
24 37 0.48
25 1 0.01
ACGTcount: A:0.11, C:0.10, G:0.21, T:0.59
Consensus pattern (24 bp):
GTTTATGTATGTTCGTTTATGTTC
Found at i:1553577 original size:34 final size:34
Alignment explanation
Indices: 1553534--1553619 Score: 163
Period size: 34 Copynumber: 2.5 Consensus size: 34
1553524 CATTTATTAT
1553534 GTTCGTTTATGTTCGTTTGTTTGAGTTCGTTTAC
1 GTTCGTTTATGTTCGTTTGTTTGAGTTCGTTTAC
*
1553568 GTTCGTTTATGTTCGTTTGTTTGTGTTCGTTTAC
1 GTTCGTTTATGTTCGTTTGTTTGAGTTCGTTTAC
1553602 GTTCGTTTATGTTCGTTT
1 GTTCGTTTATGTTCGTTT
1553620 ATCATTTAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.07, C:0.12, G:0.23, T:0.58
Consensus pattern (34 bp):
GTTCGTTTATGTTCGTTTGTTTGAGTTCGTTTAC
Found at i:1553599 original size:14 final size:14
Alignment explanation
Indices: 1553538--1553599 Score: 52
Period size: 14 Copynumber: 4.0 Consensus size: 14
1553528 TATTATGTTC
1553538 GTTTATGTTCGTTT
1 GTTTATGTTCGTTT
*
1553552 GTTTGAGTTCGTTTACGTTC
1 GTTT-A--T-G-TT-CGTTT
1553572 GTTTATGTTCGTTT
1 GTTTATGTTCGTTT
*
1553586 GTTTGTGTTCGTTT
1 GTTTATGTTCGTTT
1553600 ACGTTCGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
14 21 0.54
15 3 0.08
16 1 0.03
17 2 0.05
18 1 0.03
19 3 0.08
20 8 0.21
ACGTcount: A:0.06, C:0.10, G:0.24, T:0.60
Consensus pattern (14 bp):
GTTTATGTTCGTTT
Found at i:1558673 original size:2 final size:2
Alignment explanation
Indices: 1558666--1558695 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1558656 ATTTATTTCA
1558666 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
1558696 TTAACCAACA
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:1559442 original size:3 final size:3
Alignment explanation
Indices: 1559434--1559482 Score: 89
Period size: 3 Copynumber: 16.0 Consensus size: 3
1559424 CCAAAGATTA
1559434 AAT AAT AAT AAAT AAT 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
1559480 AAT
1 AAT
1559483 TTTAGTTAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1569748 original size:11 final size:11
Alignment explanation
Indices: 1569734--1569759 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1569724 GAAGCTAACA
1569734 AACTATTCTAG
1 AACTATTCTAG
1569745 AACTATTCTAG
1 AACTATTCTAG
1569756 AACT
1 AACT
1569760 CACACAACCC
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:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (11 bp):
AACTATTCTAG
Found at i:1572022 original size:33 final size:33
Alignment explanation
Indices: 1571980--1572044 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
1571970 GAGTAGGGGT
1571980 GACATGTGTTGGTGGAGCCTTTAGAGCATGCAC
1 GACATGTGTTGGTGGAGCCTTTAGAGCATGCAC
* *
1572013 GACATGTGTTGGTGGAGCCTTTGGAGTATGCA
1 GACATGTGTTGGTGGAGCCTTTAGAGCATGCA
1572045 TATTGTCACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.20, C:0.15, G:0.35, T:0.29
Consensus pattern (33 bp):
GACATGTGTTGGTGGAGCCTTTAGAGCATGCAC
Found at i:1578273 original size:15 final size:15
Alignment explanation
Indices: 1578250--1578283 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1578240 CGCCACAGGA
*
1578250 AGCGTCGCTAAAATC
1 AGCGCCGCTAAAATC
*
1578265 AGCGCCGCTAAAATT
1 AGCGCCGCTAAAATC
1578280 AGCG
1 AGCG
1578284 GCATTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18
Consensus pattern (15 bp):
AGCGCCGCTAAAATC
Found at i:1578507 original size:84 final size:84
Alignment explanation
Indices: 1578363--1578557 Score: 230
Period size: 84 Copynumber: 2.3 Consensus size: 84
1578353 AAATCGATAC
* * * * * * ** * *
1578363 CTATAACGGCATTTTCAGAACAAACGTCGCAAAATATTGAGATATATAGCGGTGTTTTTGGAATA
1 CTATAACGGCGTTTTTAGAACAAACGCCGTAAAAAATT-ATATATATAGCGGCATCTTTGGAACA
*
1578428 AATGCCGCAAAAGGCCGAGAT
65 AACGCCGCAAAAGGCC-AGAT
* * *
1578449 CTGTAGCGGCGTTTTT-GAATAAACGCCGTAAAAAATTATATATATAGCGGCATCTTTGGAACAA
1 CTATAACGGCGTTTTTAGAACAAACGCCGTAAAAAATTATATATATAGCGGCATCTTTGGAACAA
*
1578513 ACGCCGCAAAAGGTCAGAT
66 ACGCCGCAAAAGGCCAGAT
1578532 CTATAACGGCGTTTTTAGAACAAACG
1 CTATAACGGCGTTTTTAGAACAAACG
1578558 TCGCTAATTA
Statistics
Matches: 90, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
83 18 0.20
84 43 0.48
85 17 0.19
86 12 0.13
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (84 bp):
CTATAACGGCGTTTTTAGAACAAACGCCGTAAAAAATTATATATATAGCGGCATCTTTGGAACAA
ACGCCGCAAAAGGCCAGAT
Found at i:1578553 original size:42 final size:42
Alignment explanation
Indices: 1578311--1578557 Score: 151
Period size: 42 Copynumber: 5.8 Consensus size: 42
1578301 AAGCCGCCAT
* * * *
1578311 AAGTCAAGATCTATAGTGGCG-TTTTGGAACAAACGTCGTGAAA
1 AAGTC-AGATCTATAGCGGCGTTTTTAGAACAAACGCCG-CAAA
* * * *
1578354 AA-TC-GATACCTATAACGGCATTTTCAGAACAAACGTCGCAAA
1 AAGTCAGAT--CTATAGCGGCGTTTTTAGAACAAACGCCGCAAA
* * * * * * *
1578396 ATATTGAGATATATAGCGGTGTTTTTGGAATAAATGCCGCAAA
1 A-AGTCAGATCTATAGCGGCGTTTTTAGAACAAACGCCGCAAA
* * * * *
1578439 AGGCCGAGATCTGTAGCGGCGTTTTT-GAATAAACGCCGTAAA
1 AAGTC-AGATCTATAGCGGCGTTTTTAGAACAAACGCCGCAAA
* * * * * * *
1578481 AAATTATATATATAGCGGCATCTTTGGAACAAACGCCGCAAA
1 AAGTCAGATCTATAGCGGCGTTTTTAGAACAAACGCCGCAAA
* *
1578523 AGGTCAGATCTATAACGGCGTTTTTAGAACAAACG
1 AAGTCAGATCTATAGCGGCGTTTTTAGAACAAACG
1578558 TCGCTAATTA
Statistics
Matches: 151, Mismatches: 45, Indels: 17
0.71 0.21 0.08
Matches are distributed among these distances:
40 3 0.02
41 15 0.10
42 69 0.46
43 60 0.40
44 1 0.01
45 3 0.02
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.26
Consensus pattern (42 bp):
AAGTCAGATCTATAGCGGCGTTTTTAGAACAAACGCCGCAAA
Found at i:1581592 original size:68 final size:67
Alignment explanation
Indices: 1581478--1581613 Score: 200
Period size: 68 Copynumber: 2.0 Consensus size: 67
1581468 TTATTGCAGC
* ** * * *
1581478 GTTTGTATAAAAACGCCGCTAAAGTTATAATTTGTTGTGGCATTTATTGAAAAAACGCCACTATC
1 GTTTGTATAAAAACGCCGCTAAAGTTATAATTTATTACGGCATTTA-TCAAAAAACACCACTATA
1581543 GGT
65 GGT
*
1581546 GTTTGTATAAAAACGCCGCTAAAGTTATAATTTATTACGGCGTTTATCAAAAAACACCACTATAG
1 GTTTGTATAAAAACGCCGCTAAAGTTATAATTTATTACGGCATTTATCAAAAAACACCACTATAG
1581611 GT
66 GT
1581613 G
1 G
1581614 AACCCTATTA
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
67 19 0.31
68 42 0.69
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (67 bp):
GTTTGTATAAAAACGCCGCTAAAGTTATAATTTATTACGGCATTTATCAAAAAACACCACTATAG
GT
Found at i:1586092 original size:14 final size:14
Alignment explanation
Indices: 1586060--1586093 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1586050 GATTTCTATG
*
1586060 TAGGGAATTATTTG
1 TAGGGAATTATTTA
*
1586074 CAGGGAATTATTTA
1 TAGGGAATTATTTA
1586088 TAGGGA
1 TAGGGA
1586094 TTACTCCCCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.35
Consensus pattern (14 bp):
TAGGGAATTATTTA
Found at i:1586458 original size:18 final size:18
Alignment explanation
Indices: 1586432--1586489 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
1586422 AGCCCAAGTA
* *
1586432 CAAACAAACCCAGCAGTG
1 CAAATAAACCCAGCAGTC
*
1586450 CAAATAAACCCAGCAGCCC
1 CAAATAAACCCAGCAG-TC
*
1586469 CAAATAAACCCAACAGTC
1 CAAATAAACCCAGCAGTC
1586487 CAA
1 CAA
1586490 CCCGAATGCA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 19 0.56
19 15 0.44
ACGTcount: A:0.47, C:0.36, G:0.10, T:0.07
Consensus pattern (18 bp):
CAAATAAACCCAGCAGTC
Found at i:1587659 original size:32 final size:32
Alignment explanation
Indices: 1587572--1587660 Score: 101
Period size: 32 Copynumber: 2.7 Consensus size: 32
1587562 ATACCAATTC
*
1587572 AGTCCCTTAAATGTTTGTTTTTTTTTTCTATTTT
1 AGTCCCTTAAATG-TT-TTTTTTTTTTATATTTT
*
1587606 AG-CCACTTAAGT-TTTTGTTTTTTTTATATTTT
1 AGTCC-CTTAAATGTTTT-TTTTTTTTATATTTT
*
1587638 AGTCCTTTAAATGTTTTTTTTTT
1 AGTCCCTTAAATGTTTTTTTTTT
1587661 ATTTTAGTCC
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
31 2 0.04
32 29 0.62
33 8 0.17
34 8 0.17
ACGTcount: A:0.17, C:0.10, G:0.09, T:0.64
Consensus pattern (32 bp):
AGTCCCTTAAATGTTTTTTTTTTTTATATTTT
Found at i:1587686 original size:28 final size:28
Alignment explanation
Indices: 1587621--1587694 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
1587611 CTTAAGTTTT
* *
1587621 TGTTTTTTTTATATTTTAGTCCTTTAAA
1 TGTTTTTTTTTTATTTTAGTCCTATAAA
*
1587649 TGTTTTTTTTTTATTTTAGTCCTATAAG
1 TGTTTTTTTTTTATTTTAGTCCTATAAA
*
1587677 TTTCTATTTTTTTTATTT
1 TGT-T-TTTTTTTTATTT
1587695 ATTCAATCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 27 0.68
29 1 0.03
30 12 0.30
ACGTcount: A:0.18, C:0.07, G:0.07, T:0.69
Consensus pattern (28 bp):
TGTTTTTTTTTTATTTTAGTCCTATAAA
Found at i:1589331 original size:2 final size:2
Alignment explanation
Indices: 1589324--1589348 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1589314 TGTAGGGCAG
1589324 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 T
1589349 GAGAGGATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1590617 original size:6 final size:6
Alignment explanation
Indices: 1590606--1590677 Score: 144
Period size: 6 Copynumber: 12.0 Consensus size: 6
1590596 GATGCTACTG
1590606 TGGGAC TGGGAC TGGGAC TGGGAC TGGGAC TGGGAC TGGGAC TGGGAC
1 TGGGAC TGGGAC TGGGAC TGGGAC TGGGAC TGGGAC TGGGAC TGGGAC
1590654 TGGGAC TGGGAC TGGGAC TGGGAC
1 TGGGAC TGGGAC TGGGAC TGGGAC
1590678 ATTGTTTTCA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 66 1.00
ACGTcount: A:0.17, C:0.17, G:0.50, T:0.17
Consensus pattern (6 bp):
TGGGAC
Found at i:1591273 original size:21 final size:21
Alignment explanation
Indices: 1591200--1591273 Score: 53
Period size: 26 Copynumber: 3.2 Consensus size: 21
1591190 ATATTTTTAA
1591200 TTTAGTAATATATAATAA-ATTT
1 TTTA-TAA-ATATAATAATATTT
*
1591222 TTCATATAAT-TAATATTATCATTAT
1 TTTATA-AATATAATA--AT-ATT-T
1591247 TCTTATAAATATAATAATATTT
1 T-TTATAAATATAATAATATTT
1591269 TTTAT
1 TTTAT
1591274 TAATTATGGA
Statistics
Matches: 42, Mismatches: 2, Indels: 17
0.69 0.03 0.28
Matches are distributed among these distances:
20 5 0.12
21 8 0.19
22 7 0.17
23 3 0.07
24 5 0.12
25 5 0.12
26 9 0.21
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (21 bp):
TTTATAAATATAATAATATTT
Found at i:1598496 original size:81 final size:80
Alignment explanation
Indices: 1598361--1598522 Score: 279
Period size: 81 Copynumber: 2.0 Consensus size: 80
1598351 GGTCGTCATG
* *
1598361 CACGCCCAACGACCAAGGAGGTCGTCATGCACTAAGGGCGACCAAGGAGCGGGAGTTGCATGGTG
1 CACGCCCAACGACCAAGGAGGTCGCCATGCACTAAGGGCGACCAAGGAGCGGGAGCTGCATGGTG
1598426 TGCATGGGGGGGAGAT
66 TGCAT-GGGGGGAGAT
* *
1598442 CACGCCCAACGACCAAGGAGGTCGCCATTCACTCAGGGCGACCAAGGAGCGGGAGCTGCATGGTG
1 CACGCCCAACGACCAAGGAGGTCGCCATGCACTAAGGGCGACCAAGGAGCGGGAGCTGCATGGTG
1598507 TGCATGGGGGGAGAT
66 TGCATGGGGGGAGAT
1598522 C
1 C
1598523 GGTGCATGCA
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
80 11 0.14
81 66 0.86
ACGTcount: A:0.24, C:0.25, G:0.38, T:0.13
Consensus pattern (80 bp):
CACGCCCAACGACCAAGGAGGTCGCCATGCACTAAGGGCGACCAAGGAGCGGGAGCTGCATGGTG
TGCATGGGGGGAGAT
Found at i:1598607 original size:100 final size:100
Alignment explanation
Indices: 1598434--1598630 Score: 349
Period size: 100 Copynumber: 2.0 Consensus size: 100
1598424 TGTGCATGGG
*
1598434 GGGGAGATCACGCCCAACGACCAAGGAGGTCGCCATTCACTCAGGGCGACCAAGGAGCGGGAGCT
1 GGGGAGATCACGCCCAACGACCAAGGAGGTCGCCATTCACTCAGGGCGACCAAGGAGCAGGAGCT
*
1598499 GCATGGTGTGCATGGGGGGAGATCGGTGCATGCAT
66 GCATGGTGTACATGGGGGGAGATCGGTGCATGCAT
* *
1598534 GGGGAGATCACGCCCAACGACCAAGGAGGTCGTCATTCACTCGGGGCGACCAAGGAGCAGGAGCT
1 GGGGAGATCACGCCCAACGACCAAGGAGGTCGCCATTCACTCAGGGCGACCAAGGAGCAGGAGCT
*
1598599 GCATGGTGTATATGGGGGGAGATCGGTGCATG
66 GCATGGTGTACATGGGGGGAGATCGGTGCATG
1598631 GGGCATGCAC
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 92 1.00
ACGTcount: A:0.23, C:0.23, G:0.39, T:0.15
Consensus pattern (100 bp):
GGGGAGATCACGCCCAACGACCAAGGAGGTCGCCATTCACTCAGGGCGACCAAGGAGCAGGAGCT
GCATGGTGTACATGGGGGGAGATCGGTGCATGCAT
Found at i:1599171 original size:21 final size:21
Alignment explanation
Indices: 1599146--1599185 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1599136 TAGTTAATTA
1599146 GTTTGTTAGTATAAATTATTT
1 GTTTGTTAGTATAAATTATTT
* *
1599167 GTTTGTTAGTTTAAGTTAT
1 GTTTGTTAGTATAAATTAT
1599186 ATATTATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.17, T:0.57
Consensus pattern (21 bp):
GTTTGTTAGTATAAATTATTT
Found at i:1603427 original size:22 final size:22
Alignment explanation
Indices: 1603402--1603450 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
1603392 ACAACTAATA
*
1603402 AACTATTCTTTAATATAACTTT
1 AACTATTCTTTAATATAACGTT
1603424 AACTATTCTTTAATATAACGTT
1 AACTATTCTTTAATATAACGTT
1603446 AACTA
1 AACTA
1603451 ATAAACTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.39, C:0.14, G:0.02, T:0.45
Consensus pattern (22 bp):
AACTATTCTTTAATATAACGTT
Found at i:1603428 original size:30 final size:30
Alignment explanation
Indices: 1603394--1603519 Score: 112
Period size: 30 Copynumber: 4.4 Consensus size: 30
1603384 TCTCTTAAAC
1603394 AACTAATAAACTATTCTTTAATATAAC--T
1 AACTAATAAACTATTCTTTAATATAACTTT
*
1603422 ---T--T-AACTATTCTTTAATATAACGTT
1 AACTAATAAACTATTCTTTAATATAACTTT
*
1603446 AACTAATAAACTATTCTTTAATATAACTTA
1 AACTAATAAACTATTCTTTAATATAACTTT
1603476 AACTAATAAA-TGATT-TTTAATTATAA-TTT
1 AACTAATAAACT-ATTCTTTAA-TATAACTTT
*
1603505 ACTACTAAAAAACTA
1 A--ACTAATAAACTA
1603520 ATTAACTAAT
Statistics
Matches: 81, Mismatches: 4, Indels: 23
0.75 0.04 0.21
Matches are distributed among these distances:
22 19 0.23
23 1 0.01
24 1 0.01
25 1 0.01
27 1 0.01
29 10 0.12
30 38 0.47
31 9 0.11
32 1 0.01
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.41
Consensus pattern (30 bp):
AACTAATAAACTATTCTTTAATATAACTTT
Found at i:1603478 original size:22 final size:22
Alignment explanation
Indices: 1603400--1603480 Score: 81
Period size: 22 Copynumber: 3.3 Consensus size: 22
1603390 AAACAACTAA
1603400 TAAACTATTCTTTAATATAACT
1 TAAACTATTCTTTAATATAACT
*
1603422 TTAACTATTCTTTAATATAACGTTAACT
1 TAAACTATTCTTT-A-AT-A---TAACT
1603450 AATAAACTATTCTTTAATATAACT
1 --TAAACTATTCTTTAATATAACT
1603474 TAAACTA
1 TAAACTA
1603481 ATAAATGATT
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
22 19 0.39
23 1 0.02
24 7 0.14
25 1 0.02
27 1 0.02
28 7 0.14
29 1 0.02
30 12 0.24
ACGTcount: A:0.42, C:0.14, G:0.01, T:0.43
Consensus pattern (22 bp):
TAAACTATTCTTTAATATAACT
Found at i:1603723 original size:21 final size:21
Alignment explanation
Indices: 1603699--1603738 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1603689 TTTCTATATG
1603699 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
1603720 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
1603739 ACTAATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:1603819 original size:18 final size:18
Alignment explanation
Indices: 1603766--1603820 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
1603756 TTGTTTTACC
*
1603766 CTAATTTATAATAATAAA
1 CTAATTTATAACAATAAA
1603784 CTAA--T-TAAC--T-AA
1 CTAATTTATAACAATAAA
1603796 -TAATTTATAACAATAAA
1 CTAATTTATAACAATAAA
1603813 CTAATTTA
1 CTAATTTA
1603821 AATAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 3 0.10
12 2 0.07
13 2 0.07
14 4 0.14
15 3 0.10
16 2 0.07
17 2 0.07
18 11 0.38
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
CTAATTTATAACAATAAA
Found at i:1603879 original size:35 final size:37
Alignment explanation
Indices: 1603840--1603911 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 37
1603830 TCTTTTATAT
1603840 AACTT-AA-ACTAATAAACT-ATTTTTTATTATAATAA
1 AACTTAAACACTAATAAACTAATTTTTTA-TATAATAA
1603875 AACTTAAACTACTAATAAACTAATTTTTTATATAATA
1 AACTTAAAC-ACTAATAAACTAATTTTTTATATAATA
1603912 TAAATTCAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
35 5 0.15
36 2 0.06
38 18 0.55
39 8 0.24
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.42
Consensus pattern (37 bp):
AACTTAAACACTAATAAACTAATTTTTTATATAATAA
Found at i:1603971 original size:27 final size:29
Alignment explanation
Indices: 1603936--1604000 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
1603926 AAAATATAAC
*
1603936 TTAACTATTTA-ACTAACT-ACAAACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
1603963 TTAAATA-TTAGACTAACTAACACACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
1603991 TTAATTATTT
1 TTAAATATTT
1604001 TTTTAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 3 0.09
27 13 0.41
28 14 0.44
29 2 0.06
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (29 bp):
TTAAATATTTAGACTAACTAACAAACTAA
Found at i:1604114 original size:9 final size:9
Alignment explanation
Indices: 1604082--1604119 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
1604072 CTAACAAACT
1604082 AATAATTTAA
1 AATAA-TTAA
1604092 AATAA-TAA
1 AATAATTAA
*
1604100 ACTAATTAA
1 AATAATTAA
1604109 AATAATTAA
1 AATAATTAA
1604118 AA
1 AA
1604120 AACTTACCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 13 0.52
10 5 0.20
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (9 bp):
AATAATTAA
Found at i:1604444 original size:29 final size:28
Alignment explanation
Indices: 1604397--1604480 Score: 123
Period size: 29 Copynumber: 2.9 Consensus size: 28
1604387 AAAGGCATAG
1604397 GTCGTTGGGATCCCTTGGCGACCTACAAT
1 GTCGTTGGGATCCC-TGGCGACCTACAAT
*
1604426 GTCGCTGGGATGCCCTGGCGACCTACAAT
1 GTCGTTGGGAT-CCCTGGCGACCTACAAT
*
1604455 GTCATTGGGATTCCCTGGCGACCTAC
1 GTCGTTGGGA-TCCCTGGCGACCTAC
1604481 CCACGTTGCC
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.17, C:0.30, G:0.29, T:0.25
Consensus pattern (28 bp):
GTCGTTGGGATCCCTGGCGACCTACAAT
Found at i:1604593 original size:60 final size:60
Alignment explanation
Indices: 1604500--1604621 Score: 217
Period size: 60 Copynumber: 2.0 Consensus size: 60
1604490 CATGCTGCCA
* *
1604500 CCAGACTCATGCCACGTTGCCATGCCGCCATGCACAGCCATGCAGAGACTCCAAGCTCGC
1 CCAGACCCATGCCACGTTGCCATGCCGCCATGCACAACCATGCAGAGACTCCAAGCTCGC
*
1604560 CCAGACCCATGCCACGTTGCCATGCCGCCATGCACAACCATGCAGAGACTCCAAGCTTGC
1 CCAGACCCATGCCACGTTGCCATGCCGCCATGCACAACCATGCAGAGACTCCAAGCTCGC
1604620 CC
1 CC
1604622 GGATGCCATG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.24, C:0.41, G:0.20, T:0.15
Consensus pattern (60 bp):
CCAGACCCATGCCACGTTGCCATGCCGCCATGCACAACCATGCAGAGACTCCAAGCTCGC
Found at i:1604641 original size:29 final size:29
Alignment explanation
Indices: 1604608--1604667 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
1604598 CATGCAGAGA
*
1604608 CTCCAAGCTTGCCCGGATGCCATGGCGAC
1 CTCCAAGCTCGCCCGGATGCCATGGCGAC
1604637 CTCCAAGCTCGCCCGGATGCCATGGCGAC
1 CTCCAAGCTCGCCCGGATGCCATGGCGAC
1604666 CT
1 CT
1604668 ACGGCAACAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.17, C:0.40, G:0.27, T:0.17
Consensus pattern (29 bp):
CTCCAAGCTCGCCCGGATGCCATGGCGAC
Found at i:1609151 original size:33 final size:34
Alignment explanation
Indices: 1609080--1609167 Score: 115
Period size: 33 Copynumber: 2.6 Consensus size: 34
1609070 AATGGTAATA
*
1609080 AACAAAATTAACCAAAATACATTAACAAAAAATCC
1 AACAAAATTAA-CAAAATAAATTAACAAAAAATCC
* *
1609115 AACAAATTTAACAAAATAAATTAA-AATAAATCC
1 AACAAAATTAACAAAATAAATTAACAAAAAATCC
**
1609148 AACAAAATTAATGAAATAAA
1 AACAAAATTAACAAAATAAA
1609168 GTAAGTATTA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 25 0.53
34 12 0.26
35 10 0.21
ACGTcount: A:0.65, C:0.14, G:0.01, T:0.20
Consensus pattern (34 bp):
AACAAAATTAACAAAATAAATTAACAAAAAATCC
Found at i:1611458 original size:17 final size:18
Alignment explanation
Indices: 1611429--1611476 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
1611419 TGCAAAAAAA
*
1611429 TTAATTAAA-TAAAATA-
1 TTAAATAAATTAAAATAC
*
1611445 TTAAA-AAATTTAAATAC
1 TTAAATAAATTAAAATAC
1611462 TTAAATAAATTAAAA
1 TTAAATAAATTAAAA
1611477 ACAAAATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 3 0.12
16 10 0.38
17 5 0.19
18 8 0.31
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
TTAAATAAATTAAAATAC
Found at i:1611746 original size:51 final size:51
Alignment explanation
Indices: 1611691--1611795 Score: 138
Period size: 51 Copynumber: 2.1 Consensus size: 51
1611681 CCTCGCACTA
* * *
1611691 TACCCCACGTAGCGCCAGATCAACGTAAAGCGTGCTGTAGGGGGCGCGCCT
1 TACCCCACGTAGCGCCAGATCAACGTAAAGCATGCTGCAAGGGGCGCGCCT
* ** * *
1611742 TACCCCACGTGGTTCCATATCAACGTAAAGCATGCTGCAAGGGGCGTGCCT
1 TACCCCACGTAGCGCCAGATCAACGTAAAGCATGCTGCAAGGGGCGCGCCT
1611793 TAC
1 TAC
1611796 TGCAAAGGGC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.23, C:0.30, G:0.28, T:0.19
Consensus pattern (51 bp):
TACCCCACGTAGCGCCAGATCAACGTAAAGCATGCTGCAAGGGGCGCGCCT
Found at i:1615731 original size:8 final size:8
Alignment explanation
Indices: 1615718--1615757 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
1615708 TCATTTTCAT
1615718 AGAATTTG
1 AGAATTTG
1615726 AGAATTT-
1 AGAATTTG
*
1615733 AGAGTTTG
1 AGAATTTG
*
1615741 GGAATTTG
1 AGAATTTG
1615749 AGAATTTG
1 AGAATTTG
1615757 A
1 A
1615758 AGATTGTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.35, C:0.00, G:0.28, T:0.38
Consensus pattern (8 bp):
AGAATTTG
Found at i:1615740 original size:15 final size:15
Alignment explanation
Indices: 1615717--1615757 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1615707 CTCATTTTCA
1615717 TAGAATTTGAGAATT
1 TAGAATTTGAGAATT
* *
1615732 TAGAGTTTGGGAATT
1 TAGAATTTGAGAATT
1615747 TGAGAATTTGA
1 T-AGAATTTGA
1615758 AGATTGTGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.34, C:0.00, G:0.27, T:0.39
Consensus pattern (15 bp):
TAGAATTTGAGAATT
Found at i:1616139 original size:127 final size:126
Alignment explanation
Indices: 1615832--1616183 Score: 460
Period size: 123 Copynumber: 2.8 Consensus size: 126
1615822 GAGTACTATT
** *
1615832 CATGAAGGCGCGTTCCC-GGGGCGCTTCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCC
1 CATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAA-ATTTTATCATTGCCC
**
1615896 TATTATGTCACTCATGT-CCTCGGGGACACTAG--ATATCAGTACCTATTATTTCACTATTCA
65 TATT-TGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTAGGCA
*
1615956 CATGAA-G-GCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAAATATGTTATCATTGCC
1 CATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAAAT-T-TTATCATTG-C
* *
1616019 CCTATTTGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTC-AGGGGA
63 CCTATTTGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTA-GGCA
* * *
1616083 CATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAAATTTTATCATTTCCCT
1 CATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAAATTTTATCATTGCCCT
1616148 A--T-TCACTCATGTCCCTCGGGG--AC-AGATATATCAGTA
66 ATTTGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
1616184 AATCAGGTAA
Statistics
Matches: 206, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
120 13 0.06
121 2 0.01
122 10 0.05
123 48 0.23
124 28 0.14
125 22 0.11
126 6 0.03
127 36 0.17
128 2 0.01
129 39 0.19
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.32
Consensus pattern (126 bp):
CATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAAATTTTATCATTGCCCT
ATTTGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTAGGCA
Found at i:1616621 original size:33 final size:34
Alignment explanation
Indices: 1616560--1616634 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 34
1616550 AAATTTAATG
*
1616560 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
1616594 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
1616627 TTAAATTT
1 TTAAATTT
1616635 AAATTTAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 28 0.78
34 8 0.22
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:1617221 original size:21 final size:21
Alignment explanation
Indices: 1617191--1617284 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
1617181 TATGGTATAA
*
1617191 AACCGTGCGGGCTAGGCAAT-T
1 AACCCTGCGGGCTAGG-AATGT
1617212 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
1617233 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
*
1617254 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
1617275 AACCCTGCGG
1 AACCCTGCGG
1617285 AGATGGCATA
Statistics
Matches: 68, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
20 5 0.07
21 60 0.88
22 3 0.04
ACGTcount: A:0.21, C:0.27, G:0.34, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:1617314 original size:21 final size:21
Alignment explanation
Indices: 1617288--1617335 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1617278 CCTGCGGAGA
*
1617288 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
1617309 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
1617330 GGGCAT
1 TGGCAT
1617336 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:1617902 original size:15 final size:16
Alignment explanation
Indices: 1617882--1617912 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1617872 ACTGAAATAT
1617882 AAATATTC-AATTATA
1 AAATATTCTAATTATA
1617897 AAATATTCTAATTATA
1 AAATATTCTAATTATA
1617913 TCTAACATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATATTCTAATTATA
Found at i:1619107 original size:30 final size:34
Alignment explanation
Indices: 1619043--1619121 Score: 101
Period size: 33 Copynumber: 2.4 Consensus size: 34
1619033 TTAATAATTC
* *
1619043 TAAATAAATAATAATTATATAAATATTATTTTA-A
1 TAAA-AAATAATAATTACATAAATATTATTTAATA
*
1619077 TAAAAAATAATATTTACATAAATA-TA-TTAATA
1 TAAAAAATAATAATTACATAAATATTATTTAATA
1619109 TAAAAAATAATAA
1 TAAAAAATAATAA
1619122 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
31 3 0.08
32 15 0.38
33 18 0.45
34 4 0.10
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (34 bp):
TAAAAAATAATAATTACATAAATATTATTTAATA
Found at i:1622051 original size:21 final size:21
Alignment explanation
Indices: 1622019--1622072 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
1622009 TAAAGTACAT
*
1622019 AAAAATCG-AAATTAAATAATA
1 AAAAAT-GTAAATTAAATAAAA
*
1622040 AAAAATGTAAA-TACATAAAA
1 AAAAATGTAAATTAAATAAAA
1622060 AGAAAATGTAAAT
1 A-AAAATGTAAAT
1622073 ATACTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (21 bp):
AAAAATGTAAATTAAATAAAA
Found at i:1622052 original size:16 final size:16
Alignment explanation
Indices: 1622027--1622060 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1622017 ATAAAAATCG
1622027 AAATTAAATA-ATAAA
1 AAATTAAATACATAAA
1622042 AAATGTAAATACATAAA
1 AAAT-TAAATACATAAA
1622059 AA
1 AA
1622061 GAAAATGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 6 0.35
17 7 0.41
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (16 bp):
AAATTAAATACATAAA
Found at i:1622882 original size:19 final size:18
Alignment explanation
Indices: 1622860--1622922 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 18
1622850 AATAATATAC
1622860 TATTATTAATTATATATGT
1 TATTATTAATTATATAT-T
1622879 TATTATTATTATTATATATT
1 TATTATTA--ATTATATATT
*
1622899 AATTATATATATTATTATATT
1 TATTAT-TA-ATTA-TATATT
1622920 TAT
1 TAT
1622923 AAATATTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
19 8 0.21
20 11 0.29
21 19 0.50
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
TATTATTAATTATATATT
Found at i:1622904 original size:23 final size:20
Alignment explanation
Indices: 1622860--1622918 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 20
1622850 AATAATATAC
*
1622860 TATTATTAATTATATATGTTA
1 TATTATT-ATTATATATATTA
1622881 TTATTATTATTATATATTAATTA
1 -TATTATTATTATATA-T-ATTA
1622904 TATATATTATTATAT
1 TAT-TATTATTATAT
1622919 TTATAAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
21 8 0.24
22 11 0.33
23 14 0.42
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TATTATTATTATATATATTA
Found at i:1625384 original size:23 final size:21
Alignment explanation
Indices: 1625336--1625390 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 21
1625326 ACATATAGCT
*
1625336 TCTTTTCATGTAATTCATATA
1 TCTTTTCATATAATTCATATA
* *
1625357 ACTTTTCATATAATTCACATATC
1 TCTTTTCATATAATT--CATATA
1625380 TCTTTTCATAT
1 TCTTTTCATAT
1625391 TCTCATAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 13 0.46
23 15 0.54
ACGTcount: A:0.29, C:0.18, G:0.02, T:0.51
Consensus pattern (21 bp):
TCTTTTCATATAATTCATATA
Found at i:1625894 original size:24 final size:20
Alignment explanation
Indices: 1625837--1625913 Score: 68
Period size: 20 Copynumber: 3.7 Consensus size: 20
1625827 TTCCCCTTGA
*
1625837 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATCCTAC
*
1625857 AGTGTATCGATGCATCCCTTAAC
1 AGTGCATCGATGCAT-CC-T-AC
*
1625880 ATGTGCATCGATGCACTCCT-T
1 A-GTGCATCGATGCA-TCCTAC
1625901 A-TGCATCGATGCA
1 AGTGCATCGATGCA
1625914 CTAATTGCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
19 12 0.25
20 14 0.29
21 2 0.04
22 1 0.02
23 4 0.08
24 14 0.29
25 1 0.02
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (20 bp):
AGTGCATCGATGCATCCTAC
Found at i:1645284 original size:3 final size:3
Alignment explanation
Indices: 1645278--1645363 Score: 61
Period size: 3 Copynumber: 27.0 Consensus size: 3
1645268 TATAATAATA
* *
1645278 TAT TAT TAT TAAT TA- TAT ATGT TAC TAT TAT TAT TAT TAT ATAT TAAT
1 TAT TAT TAT T-AT TAT TAT -TAT TAT TAT TAT TAT TAT TAT -TAT T-AT
1645326 TA- TAT ATAT TAT TAT ATAT TAAT TA- TAT ATAT TAT TAT
1 TAT TAT -TAT TAT TAT -TAT T-AT TAT TAT -TAT TAT TAT
1645364 ATTTACAAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 22
0.72 0.04 0.23
Matches are distributed among these distances:
2 6 0.09
3 39 0.57
4 23 0.34
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:1645331 original size:13 final size:12
Alignment explanation
Indices: 1645284--1645365 Score: 89
Period size: 12 Copynumber: 6.9 Consensus size: 12
1645274 AATATATTAT
1645284 TATTAATTATATA
1 TATT-ATTATATA
* *
1645297 TGTTACTAT-TA
1 TATTATTATATA
1645308 TTATTATTATATA
1 -TATTATTATATA
*
1645321 T-TAATTATATA
1 TATTATTATATA
1645332 TATTATTATATA
1 TATTATTATATA
*
1645344 T-TAATTATATA
1 TATTATTATATA
1645355 TATTATTATAT
1 TATTATTATAT
1645366 TTACAAATAT
Statistics
Matches: 57, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
11 22 0.39
12 30 0.53
13 5 0.09
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (12 bp):
TATTATTATATA
Found at i:1645339 original size:23 final size:23
Alignment explanation
Indices: 1645309--1645365 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
1645299 TTACTATTAT
1645309 TATTATTATATATTAATTATATA
1 TATTATTATATATTAATTATATA
1645332 TATTATTATATATTAATTATATA
1 TATTATTATATATTAATTATATA
1645355 TATTATTATAT
1 TATTATTATAT
1645366 TTACAAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TATTATTATATATTAATTATATA
Found at i:1651723 original size:6 final size:6
Alignment explanation
Indices: 1651712--1651736 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1651702 CTGTCTCGGC
1651712 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
1651737 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:1652037 original size:22 final size:22
Alignment explanation
Indices: 1652012--1652053 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1652002 AGGATTTATT
* *
1652012 TGATTTAATTTCAGGGGTTACA
1 TGATATAATTTCAGGAGTTACA
1652034 TGATATAATTTCAGGAGTTA
1 TGATATAATTTCAGGAGTTA
1652054 TAACAGCTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.40
Consensus pattern (22 bp):
TGATATAATTTCAGGAGTTACA
Found at i:1652695 original size:10 final size:11
Alignment explanation
Indices: 1652675--1652708 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 11
1652665 TATTTTTTGG
1652675 AAAGAAAAAAA
1 AAAGAAAAAAA
1652686 AAAGAAAAAAA
1 AAAGAAAAAAA
1652697 ATAAGAAGAAAA
1 A-AAGAA-AAAA
1652709 TGGGTGTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 12 0.57
12 5 0.24
13 4 0.19
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:1658037 original size:29 final size:29
Alignment explanation
Indices: 1657995--1658073 Score: 149
Period size: 29 Copynumber: 2.7 Consensus size: 29
1657985 CGGTGACCGG
*
1657995 TATATTTATCGATCTAACACCAGTCAGAC
1 TATATTTTTCGATCTAACACCAGTCAGAC
1658024 TATATTTTTCGATCTAACACCAGTCAGAC
1 TATATTTTTCGATCTAACACCAGTCAGAC
1658053 TATATTTTTCGATCTAACACC
1 TATATTTTTCGATCTAACACC
1658074 CTTTACAGTA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.32, C:0.24, G:0.09, T:0.35
Consensus pattern (29 bp):
TATATTTTTCGATCTAACACCAGTCAGAC
Found at i:1658447 original size:19 final size:18
Alignment explanation
Indices: 1658420--1658456 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1658410 TCTTATTAAC
1658420 GTATATTTTAATATATTTA
1 GTATATTTTAATA-ATTTA
*
1658439 GTATTTTTTAATAATTTA
1 GTATATTTTAATAATTTA
1658457 TTTAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (18 bp):
GTATATTTTAATAATTTA
Found at i:1665523 original size:2 final size:2
Alignment explanation
Indices: 1665518--1665554 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1665508 CATTCATTCA
1665518 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 A
1665555 AGGCATTCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1672405 original size:15 final size:14
Alignment explanation
Indices: 1672377--1672422 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
1672367 GTCGTGAGTG
1672377 TTTTTTTG-TTTAT
1 TTTTTTTGTTTTAT
1672390 TTTTATTTGTTTTAT
1 TTTT-TTTGTTTTAT
*
1672405 TTTTTTAGTTTTAAT
1 TTTTTTTGTTTT-AT
1672420 TTT
1 TTT
1672423 AATATTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 4 0.14
14 11 0.38
15 14 0.48
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (14 bp):
TTTTTTTGTTTTAT
Found at i:1672416 original size:23 final size:22
Alignment explanation
Indices: 1672375--1672417 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1672365 TTGTCGTGAG
*
1672375 TGTTTTTTTGTTTATTTTTATT
1 TGTTTTTTTGTTTAGTTTTATT
*
1672397 TGTTTTATTTTTTTAGTTTTA
1 TGTTTT-TTTGTTTAGTTTTA
1672418 ATTTTAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.79
Consensus pattern (22 bp):
TGTTTTTTTGTTTAGTTTTATT
Found at i:1674727 original size:23 final size:23
Alignment explanation
Indices: 1674700--1674748 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
1674690 GTGGTGTTGG
1674700 TTTAATGG-ATATTTTAACTTTAT
1 TTTAATGGTATA-TTTAACTTTAT
*
1674723 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
1674746 TTT
1 TTT
1674749 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 21 0.88
24 3 0.12
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.59
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:1677125 original size:2 final size:2
Alignment explanation
Indices: 1677118--1677153 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1677108 TAGGTTGTTA
1677118 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
1677154 TAACTCTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.