Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 5 of 284
Found at i:1442905 original size:23 final size:23
Alignment explanation
Indices: 1442879--1442933 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
1442869 AGAAATATAT
*
1442879 AAAAAAAATACAT-AAATATTTAA
1 AAAAAAAATA-ATAAAAAATTTAA
*
1442902 AAAAAACATAATAAAAAATTTAA
1 AAAAAAAATAATAAAAAATTTAA
1442925 AAAATAAAA
1 AAAA-AAAA
1442934 AAATTGTTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.07
23 22 0.81
24 3 0.11
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.22
Consensus pattern (23 bp):
AAAAAAAATAATAAAAAATTTAA
Found at i:1451456 original size:16 final size:17
Alignment explanation
Indices: 1451422--1451463 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1451412 TTTTTAAAAC
*
1451422 ATAATTTTTTTGTTCAA
1 ATAATTTTTTTGTTAAA
1451439 ATAATTTTTTTG-TAAA
1 ATAATTTTTTTGTTAAA
*
1451455 ATTATTTTT
1 ATAATTTTT
1451464 CGAAAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (17 bp):
ATAATTTTTTTGTTAAA
Found at i:1451572 original size:18 final size:18
Alignment explanation
Indices: 1451549--1451589 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
1451539 TTGAAATCGG
1451549 CTTTTTTACA-AAAAAAAA
1 CTTTTTTA-ATAAAAAAAA
*
1451567 C-TTTTTAATAGAAAAAA
1 CTTTTTTAATAAAAAAAA
1451584 CTTTTT
1 CTTTTT
1451590 GGACTAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 1 0.05
17 14 0.70
18 5 0.25
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.41
Consensus pattern (18 bp):
CTTTTTTAATAAAAAAAA
Found at i:1452733 original size:21 final size:20
Alignment explanation
Indices: 1452688--1452729 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1452678 TTTATAATTT
*
1452688 TACTTGTAAACTCCTAAAAA
1 TACTTGTAAACTCCAAAAAA
1452708 TACTTGTAAACTCCAAAAAA
1 TACTTGTAAACTCCAAAAAA
1452728 TA
1 TA
1452730 ACTTTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.48, C:0.19, G:0.05, T:0.29
Consensus pattern (20 bp):
TACTTGTAAACTCCAAAAAA
Found at i:1459389 original size:37 final size:37
Alignment explanation
Indices: 1459347--1459427 Score: 135
Period size: 37 Copynumber: 2.2 Consensus size: 37
1459337 CGGGGTTTCA
* *
1459347 ACCCGGATAAAATCTCCACACGTGGTCATCGGGTCTT
1 ACCCGGACAAAATCTCCACACGTAGTCATCGGGTCTT
*
1459384 ACCCGGACAGAATCTCCACACGTAGTCATCGGGTCTT
1 ACCCGGACAAAATCTCCACACGTAGTCATCGGGTCTT
1459421 ACCCGGA
1 ACCCGGA
1459428 ATATATTTCC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.25, C:0.32, G:0.22, T:0.21
Consensus pattern (37 bp):
ACCCGGACAAAATCTCCACACGTAGTCATCGGGTCTT
Found at i:1459701 original size:48 final size:48
Alignment explanation
Indices: 1459553--1459711 Score: 194
Period size: 48 Copynumber: 3.3 Consensus size: 48
1459543 GATCATTCGG
* * * *
1459553 CCACAATATACACATCTCCTACGTAT-TGCACATTAGCCATTCGGCTTTA
1 CCAC-ATATACATATCTCATACATATCT-CATATTAGCCATTCGGCTTTA
* * * *
1459602 CCAAATATACATCTCTCATACATATTTCATATTAGCCATTTGGCTTTA
1 CCACATATACATATCTCATACATATCTCATATTAGCCATTCGGCTTTA
*
1459650 CCACATATACATATCTCATACATGTCTCATATTAGCCATTCGGCTTTA
1 CCACATATACATATCTCATACATATCTCATATTAGCCATTCGGCTTTA
* *
1459698 CCACACATATATAT
1 CCACATATACATAT
1459712 ATTTACCTTG
Statistics
Matches: 95, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
48 91 0.96
49 4 0.04
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.35
Consensus pattern (48 bp):
CCACATATACATATCTCATACATATCTCATATTAGCCATTCGGCTTTA
Found at i:1464019 original size:31 final size:29
Alignment explanation
Indices: 1463925--1464022 Score: 96
Period size: 31 Copynumber: 3.4 Consensus size: 29
1463915 TAATCACATC
1463925 AATATTAAATTAATAAAATATTATCAAGATA
1 AATATTAAATTAATAAAATA-TATC-AGATA
* * *
1463956 AATATTTAATT--T--AATATATCATATT
1 AATATTAAATTAATAAAATATATCAGATA
*
1463981 AATATTAAATTAATAAAATACTCTCTAGATA
1 AATATTAAATTAATAAAATA-TATC-AGATA
1464012 AATATTAAATT
1 AATATTAAATT
1464023 TAATTTAATA
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
25 13 0.24
26 4 0.07
27 5 0.09
29 5 0.09
30 3 0.06
31 24 0.44
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (29 bp):
AATATTAAATTAATAAAATATATCAGATA
Found at i:1464424 original size:17 final size:17
Alignment explanation
Indices: 1464402--1464435 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1464392 GAGCATTTGA
1464402 TTCAAATACTGAGAAGG
1 TTCAAATACTGAGAAGG
1464419 TTCAAATACTGAGAAGG
1 TTCAAATACTGAGAAGG
1464436 ATTATTATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.24
Consensus pattern (17 bp):
TTCAAATACTGAGAAGG
Found at i:1465427 original size:19 final size:19
Alignment explanation
Indices: 1465393--1465444 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
1465383 GAATTTTTAG
* * *
1465393 AAAATTAATTTGATCAAGT
1 AAAATTAAATTAATCAAAT
1465412 AAAATTAAATTAATCAAAT
1 AAAATTAAATTAATCAAAT
* *
1465431 TAAATAAAATTAAT
1 AAAATTAAATTAAT
1465445 ATGATATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (19 bp):
AAAATTAAATTAATCAAAT
Found at i:1465915 original size:31 final size:29
Alignment explanation
Indices: 1465880--1465937 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 29
1465870 TATAGTATTT
*
1465880 TATTAATTTAATATTAAAGTGATTATCTTAA
1 TATTAAATTAA-ATTAAA-TGATTATCTTAA
* *
1465911 TATTAAATTAAATTTAATGTTTATCTT
1 TATTAAATTAAATTAAATGATTATCTT
1465938 GTAAATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.38
30 5 0.21
31 10 0.42
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (29 bp):
TATTAAATTAAATTAAATGATTATCTTAA
Found at i:1468220 original size:23 final size:25
Alignment explanation
Indices: 1468189--1468235 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
1468179 TAAATTAGAA
1468189 AAATATCTC-T-AGA-AATTTTCTT
1 AAATATCTCTTCAGAGAATTTTCTT
1468211 AAATAATCTCTTCAGAGAATTTTCT
1 AAAT-ATCTCTTCAGAGAATTTTCT
1468236 CTCTACAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 4 0.19
23 5 0.24
24 1 0.05
25 3 0.14
26 8 0.38
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.43
Consensus pattern (25 bp):
AAATATCTCTTCAGAGAATTTTCTT
Found at i:1468394 original size:12 final size:13
Alignment explanation
Indices: 1468377--1468406 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1468367 TCAAGATAAA
1468377 TATTATTAAAT-T
1 TATTATTAAATCT
1468389 TATTATTAAATCT
1 TATTATTAAATCT
1468402 TATTA
1 TATTA
1468407 AAATAATAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (13 bp):
TATTATTAAATCT
Found at i:1468414 original size:57 final size:58
Alignment explanation
Indices: 1468345--1468475 Score: 142
Period size: 60 Copynumber: 2.2 Consensus size: 58
1468335 ATCACTTTAA
* * * *
1468345 TATTAAATTAATATAATATTTA-T-CAAGATAAATATT-ATTAAATTTATTATTAAATCT
1 TATTAAAATAATATAATATTTACTACAAGATAAACATTAATTAAATTTAATATTAAA--G
* * *
1468402 TATTAAAATAATAGAATGTTTATCTACAAGATAAACATTAAATTTAATTTAATATTAAAG
1 TATTAAAATAATATAATATTTA-CTACAAGATAAACATT-AATTAAATTTAATATTAAAG
1468462 TATTAAAATAATAT
1 TATTAAAATAATAT
1468476 TATTTTTGGA
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
57 19 0.31
59 1 0.02
60 25 0.41
62 16 0.26
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (58 bp):
TATTAAAATAATATAATATTTACTACAAGATAAACATTAATTAAATTTAATATTAAAG
Found at i:1468869 original size:21 final size:20
Alignment explanation
Indices: 1468832--1468871 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1468822 CACTTGAAGC
**
1468832 AGGGCACACGCTTGTGTGGA
1 AGGGCACACGCCCGTGTGGA
1468852 AGGGCAACACGCCCGTGTGG
1 AGGGC-ACACGCCCGTGTGG
1468872 CCATTATGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.20, C:0.25, G:0.40, T:0.15
Consensus pattern (20 bp):
AGGGCACACGCCCGTGTGGA
Found at i:1470113 original size:12 final size:12
Alignment explanation
Indices: 1470096--1470123 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1470086 GATACGTCTT
1470096 ATATTGACTTTC
1 ATATTGACTTTC
1470108 ATATTGACTTTC
1 ATATTGACTTTC
1470120 ATAT
1 ATAT
1470124 AAGGAGGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (12 bp):
ATATTGACTTTC
Found at i:1470290 original size:46 final size:48
Alignment explanation
Indices: 1470183--1470304 Score: 158
Period size: 46 Copynumber: 2.6 Consensus size: 48
1470173 AGCTGACGCT
* * *
1470183 ATGTCCCAGACAGGTCTTACACTAGCTTGTATATCCCGAGGCCGATGC
1 ATGTCCCAGACATGTCTTACACTAGCTTCTATATCCCAAGGCCGATGC
* * * *
1470231 ATATCCCAGACATGTCTTACACTAGC-TCT-TGTCTCAATGCCGATGC
1 ATGTCCCAGACATGTCTTACACTAGCTTCTATATCCCAAGGCCGATGC
*
1470277 ATGTCCCAGACATGTCTTACACTGGCTT
1 ATGTCCCAGACATGTCTTACACTAGCTT
1470305 ACATACCACC
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
46 37 0.58
47 3 0.05
48 24 0.38
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.29
Consensus pattern (48 bp):
ATGTCCCAGACATGTCTTACACTAGCTTCTATATCCCAAGGCCGATGC
Found at i:1472468 original size:74 final size:74
Alignment explanation
Indices: 1472347--1472493 Score: 285
Period size: 74 Copynumber: 2.0 Consensus size: 74
1472337 TATGTTTCAT
1472347 TCCATGCATTTCCAAATTTACATTAAACACGCTTAACATTATAAACAAAACTAAATAAACCATTA
1 TCCATGCATTTCCAAATTTACATTAAACACGCTTAACATTATAAACAAAACTAAATAAACCATTA
1472412 CCAAACATA
66 CCAAACATA
*
1472421 TCCATGCATTTCCAAATTTACATTAAACACGCTTAGCATTATAAACAAAACTAAATAAACCATTA
1 TCCATGCATTTCCAAATTTACATTAAACACGCTTAACATTATAAACAAAACTAAATAAACCATTA
1472486 CCAAACAT
66 CCAAACAT
1472494 GTTATTATAC
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.46, C:0.23, G:0.03, T:0.27
Consensus pattern (74 bp):
TCCATGCATTTCCAAATTTACATTAAACACGCTTAACATTATAAACAAAACTAAATAAACCATTA
CCAAACATA
Found at i:1472723 original size:64 final size:64
Alignment explanation
Indices: 1472650--1472780 Score: 253
Period size: 64 Copynumber: 2.0 Consensus size: 64
1472640 TTACATATTC
1472650 TAAACTCATCATTCCAATATATTTCATTCAACCAAAAACCTAACCGAAACAAATAATTATTTCA
1 TAAACTCATCATTCCAATATATTTCATTCAACCAAAAACCTAACCGAAACAAATAATTATTTCA
*
1472714 TAAACTCATCATTCCAATATATTTCATTCAACCAAAAATCTAACCGAAACAAATAATTATTTCA
1 TAAACTCATCATTCCAATATATTTCATTCAACCAAAAACCTAACCGAAACAAATAATTATTTCA
1472778 TAA
1 TAA
1472781 TATATATATA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.31
Consensus pattern (64 bp):
TAAACTCATCATTCCAATATATTTCATTCAACCAAAAACCTAACCGAAACAAATAATTATTTCA
Found at i:1473360 original size:51 final size:51
Alignment explanation
Indices: 1473284--1473384 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
1473274 GTTTATCTTA
1473284 GTAAGAAATCTCAGAGGGTGACTAAGGATCAAATCAAATTGCGTGCTTTCC
1 GTAAGAAATCTCAGAGGGTGACTAAGGATCAAATCAAATTGCGTGCTTTCC
*
1473335 GTAAGAAATCTCAGAGGGTGACTAAGGATTAAATCAAATTGCGTGCTTTC
1 GTAAGAAATCTCAGAGGGTGACTAAGGATCAAATCAAATTGCGTGCTTTC
1473385 TTTTTTTCCC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.27
Consensus pattern (51 bp):
GTAAGAAATCTCAGAGGGTGACTAAGGATCAAATCAAATTGCGTGCTTTCC
Found at i:1478009 original size:42 final size:42
Alignment explanation
Indices: 1477963--1478178 Score: 156
Period size: 42 Copynumber: 5.1 Consensus size: 42
1477953 GGCTCGGAGC
1477963 CCGATAATATTCACCAGCTTAAAGCTTGCTAGACCTTTAAGT
1 CCGATAATATTCACCAGCTTAAAGCTTGCTAGACCTTTAAGT
** * * * *** *
1478005 CCGAT-ATCATGTCACTGGCATT-ACGCCTGCTAG-GCTCGGAGC
1 CCGATAAT-AT-TCACCAGC-TTAAAGCTTGCTAGACCTTTAAGT
1478047 CCGATAATATTCACCAGCTTAAAGCTTGCTAGACCTTTAAGT
1 CCGATAATATTCACCAGCTTAAAGCTTGCTAGACCTTTAAGT
** * * * *** *
1478089 CCGAT-ATCATGTCACTGGCATT-ACGCCTGCTAG-GCTCGGAGC
1 CCGATAAT-AT-TCACCAGC-TTAAAGCTTGCTAGACCTTTAAGT
*
1478131 CCGATAATATTCACCAGCTTAAAGCTTTCTAGACCTTTAAGT
1 CCGATAATATTCACCAGCTTAAAGCTTGCTAGACCTTTAAGT
*
1478173 TCGATA
1 CCGATA
1478179 TCATTTCACC
Statistics
Matches: 124, Mismatches: 38, Indels: 24
0.67 0.20 0.13
Matches are distributed among these distances:
40 4 0.03
41 33 0.27
42 49 0.40
43 34 0.27
44 4 0.03
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (42 bp):
CCGATAATATTCACCAGCTTAAAGCTTGCTAGACCTTTAAGT
Found at i:1478229 original size:84 final size:84
Alignment explanation
Indices: 1477900--1478209 Score: 548
Period size: 84 Copynumber: 3.7 Consensus size: 84
1477890 CACCGACAAT
* *
1477900 AAGCCTGCTAGACCTTTAAGTCCGATATCATTTCACCGGCATTACGCCTGCTAGGCTCGGAGCCC
1 AAGCTTGCTAGACCTTTAAGTCCGATATCATGTCACCGGCATTACGCCTGCTAGGCTCGGAGCCC
1477965 GATAATATTCACCAGCTTA
66 GATAATATTCACCAGCTTA
*
1477984 AAGCTTGCTAGACCTTTAAGTCCGATATCATGTCACTGGCATTACGCCTGCTAGGCTCGGAGCCC
1 AAGCTTGCTAGACCTTTAAGTCCGATATCATGTCACCGGCATTACGCCTGCTAGGCTCGGAGCCC
1478049 GATAATATTCACCAGCTTA
66 GATAATATTCACCAGCTTA
*
1478068 AAGCTTGCTAGACCTTTAAGTCCGATATCATGTCACTGGCATTACGCCTGCTAGGCTCGGAGCCC
1 AAGCTTGCTAGACCTTTAAGTCCGATATCATGTCACCGGCATTACGCCTGCTAGGCTCGGAGCCC
1478133 GATAATATTCACCAGCTTA
66 GATAATATTCACCAGCTTA
* * * *
1478152 AAGCTTTCTAGACCTTTAAGTTCGATATCATTTCACCGGCATTATGCCTGCTAGGCTC
1 AAGCTTGCTAGACCTTTAAGTCCGATATCATGTCACCGGCATTACGCCTGCTAGGCTC
1478210 AAAGCCCAAA
Statistics
Matches: 218, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 218 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (84 bp):
AAGCTTGCTAGACCTTTAAGTCCGATATCATGTCACCGGCATTACGCCTGCTAGGCTCGGAGCCC
GATAATATTCACCAGCTTA
Found at i:1480128 original size:14 final size:15
Alignment explanation
Indices: 1480099--1480128 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1480089 CAAAATTAAG
1480099 ACATGATACTTTCAC
1 ACATGATACTTTCAC
1480114 ACATGATAC-TTCAC
1 ACATGATACTTTCAC
1480128 A
1 A
1480129 TATAATAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30
Consensus pattern (15 bp):
ACATGATACTTTCAC
Found at i:1485181 original size:7 final size:8
Alignment explanation
Indices: 1485153--1485181 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1485143 AAAAATTTTA
1485153 AAAAAAGG
1 AAAAAAGG
1485161 AAAAAAGG
1 AAAAAAGG
1485169 AAAAAA-G
1 AAAAAAGG
1485176 AAAAAA
1 AAAAAA
1485182 AAAGAAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:1485792 original size:14 final size:14
Alignment explanation
Indices: 1485775--1485814 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
1485765 AGGATAATTG
1485775 TTAGATTTTATTAT
1 TTAGATTTTATTAT
1485789 TTAGATTTTATTAT
1 TTAGATTTTATTAT
1485803 TTAGATTTTATT
1 TTAGATTTTATT
1485815 TTAGCTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (14 bp):
TTAGATTTTATTAT
Found at i:1485836 original size:10 final size:10
Alignment explanation
Indices: 1485821--1485869 Score: 71
Period size: 10 Copynumber: 4.9 Consensus size: 10
1485811 TATTTTAGCT
1485821 TTTATCTTTA
1 TTTATCTTTA
1485831 TTTATCTTTA
1 TTTATCTTTA
*
1485841 ATTATCTTTA
1 TTTATCTTTA
* *
1485851 ATTATCTGTA
1 TTTATCTTTA
1485861 TTTATCTTT
1 TTTATCTTT
1485870 TAGAATTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 35 1.00
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.65
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:1486609 original size:18 final size:18
Alignment explanation
Indices: 1486586--1486620 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1486576 TATTCTCTAT
*
1486586 TTTAATTTTCGCAATTTA
1 TTTAATTTTCACAATTTA
1486604 TTTAATTTTCACAATTT
1 TTTAATTTTCACAATTT
1486621 CAATCAACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.11, G:0.03, T:0.57
Consensus pattern (18 bp):
TTTAATTTTCACAATTTA
Found at i:1487519 original size:25 final size:25
Alignment explanation
Indices: 1487491--1487568 Score: 104
Period size: 25 Copynumber: 3.1 Consensus size: 25
1487481 CTTATTCGAA
* *
1487491 CTGAATATTAGTAAGCTCTTACAAG
1 CTGAATATTGGTAAGCTCTTACGAG
1487516 CTGAATATTGGTAAGCTTCTT-CGAG
1 CTGAATATTGGTAAGC-TCTTACGAG
* *
1487541 CTGAATAATGGTAAGCTCATACGAG
1 CTGAATATTGGTAAGCTCTTACGAG
1487566 CTG
1 CTG
1487569 TGGTGAGTCT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
24 3 0.06
25 40 0.85
26 4 0.09
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (25 bp):
CTGAATATTGGTAAGCTCTTACGAG
Found at i:1487765 original size:45 final size:45
Alignment explanation
Indices: 1487709--1487799 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
1487699 CAATAATTAC
*
1487709 TAAATTATATAAATACACAGTGTAATTATACGAACTTACCTCGAA
1 TAAAGTATATAAATACACAGTGTAATTATACGAACTTACCTCGAA
1487754 TAAAGTATATAAATACACAGTGTAATTATACGAACTTACCTCGAA
1 TAAAGTATATAAATACACAGTGTAATTATACGAACTTACCTCGAA
1487799 T
1 T
1487800 CAGTACAGAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (45 bp):
TAAAGTATATAAATACACAGTGTAATTATACGAACTTACCTCGAA
Found at i:1491617 original size:17 final size:17
Alignment explanation
Indices: 1491595--1491628 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1491585 ACTCAGAAAG
1491595 AAGGCATTGATTTTATA
1 AAGGCATTGATTTTATA
1491612 AAGGCATTGATTTTATA
1 AAGGCATTGATTTTATA
1491629 GAGACTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (17 bp):
AAGGCATTGATTTTATA
Found at i:1498411 original size:105 final size:107
Alignment explanation
Indices: 1498279--1498490 Score: 410
Period size: 107 Copynumber: 2.0 Consensus size: 107
1498269 ATATATAATA
1498279 GTAAATAATATCACATCATT-AAAAAAAAG-AAAAAAAAACTCAAGAGTTAGATGAAATGACAAA
1 GTAAATAATATCACATCATTAAAAAAAAAGAAAAAAAAAACTCAAGAGTTAGATGAAATGACAAA
1498342 AGTTCTTTTCTACCTTAATCAATAGTCGAGAGTTTGATCCTC
66 AGTTCTTTTCTACCTTAATCAATAGTCGAGAGTTTGATCCTC
1498384 GTAAATAATATCACATCATTAAAAAAAAAGAAAAAAAAAACTCAAGAGTTAGATGAAATGACAAA
1 GTAAATAATATCACATCATTAAAAAAAAAGAAAAAAAAAACTCAAGAGTTAGATGAAATGACAAA
1498449 AGTTCTTTTCTACCTTAATCAATAGTCGAGAGTTTGATCCTC
66 AGTTCTTTTCTACCTTAATCAATAGTCGAGAGTTTGATCCTC
1498491 ACCCTAAATA
Statistics
Matches: 105, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
105 20 0.19
106 9 0.09
107 76 0.72
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.27
Consensus pattern (107 bp):
GTAAATAATATCACATCATTAAAAAAAAAGAAAAAAAAAACTCAAGAGTTAGATGAAATGACAAA
AGTTCTTTTCTACCTTAATCAATAGTCGAGAGTTTGATCCTC
Found at i:1500834 original size:69 final size:69
Alignment explanation
Indices: 1500723--1501000 Score: 556
Period size: 69 Copynumber: 4.0 Consensus size: 69
1500713 AATTTGTTAA
1500723 ATCAAGAATCAATGGTCTGACCTATTCAACCATCAGTCAAGTTATTAAAACAATGAATATGACAT
1 ATCAAGAATCAATGGTCTGACCTATTCAACCATCAGTCAAGTTATTAAAACAATGAATATGACAT
1500788 TTTG
66 TTTG
1500792 ATCAAGAATCAATGGTCTGACCTATTCAACCATCAGTCAAGTTATTAAAACAATGAATATGACAT
1 ATCAAGAATCAATGGTCTGACCTATTCAACCATCAGTCAAGTTATTAAAACAATGAATATGACAT
1500857 TTTG
66 TTTG
1500861 ATCAAGAATCAATGGTCTGACCTATTCAACCATCAGTCAAGTTATTAAAACAATGAATATGACAT
1 ATCAAGAATCAATGGTCTGACCTATTCAACCATCAGTCAAGTTATTAAAACAATGAATATGACAT
1500926 TTTG
66 TTTG
1500930 ATCAAGAATCAATGGTCTGACCTATTCAACCATCAGTCAAGTTATTAAAACAATGAATATGACAT
1 ATCAAGAATCAATGGTCTGACCTATTCAACCATCAGTCAAGTTATTAAAACAATGAATATGACAT
1500995 TTTG
66 TTTG
1500999 AT
1 AT
1501001 ATTATACCTC
Statistics
Matches: 209, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 209 1.00
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (69 bp):
ATCAAGAATCAATGGTCTGACCTATTCAACCATCAGTCAAGTTATTAAAACAATGAATATGACAT
TTTG
Found at i:1504958 original size:38 final size:38
Alignment explanation
Indices: 1504913--1504988 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
1504903 TTTCAATGCT
1504913 CATTCCAATTCATAATCAATATCTTTCAATATCAATCA
1 CATTCCAATTCATAATCAATATCTTTCAATATCAATCA
*
1504951 CATTCCAATTCATAGTCAATATCTTTCAATATCAATCA
1 CATTCCAATTCATAATCAATATCTTTCAATATCAATCA
1504989 ATTGATCAAT
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:0.38, C:0.24, G:0.01, T:0.37
Consensus pattern (38 bp):
CATTCCAATTCATAATCAATATCTTTCAATATCAATCA
Found at i:1505303 original size:27 final size:27
Alignment explanation
Indices: 1505273--1505329 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
1505263 AACTCACATT
1505273 TCAATTTCCAAAT-AATATCA-ATTTCAA
1 TCAA-TTCCAAATCAATA-CACATTTCAA
*
1505300 TCAATTCCAATTCAATACACATTTCAA
1 TCAATTCCAAATCAATACACATTTCAA
1505327 TCA
1 TCA
1505330 GTCTCATGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 9 0.33
27 18 0.67
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (27 bp):
TCAATTCCAAATCAATACACATTTCAA
Found at i:1511535 original size:38 final size:37
Alignment explanation
Indices: 1511476--1511554 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 37
1511466 AACATAACGT
* * **
1511476 TATTTGGGCTCTGTGCCTAGCAGGCTTTGTGTCGGTG
1 TATTCGGGCTCTGTACCTAGCAGGCTTCATGTCGGTG
*
1511513 ATATTCGGGCTCTGTACGTAGCAGGCTTCATGTCGGTG
1 -TATTCGGGCTCTGTACCTAGCAGGCTTCATGTCGGTG
1511551 TATT
1 TATT
1511555 ATATCAGGCT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 4 0.11
38 32 0.89
ACGTcount: A:0.13, C:0.19, G:0.32, T:0.37
Consensus pattern (37 bp):
TATTCGGGCTCTGTACCTAGCAGGCTTCATGTCGGTG
Found at i:1511738 original size:41 final size:41
Alignment explanation
Indices: 1511482--1511749 Score: 251
Period size: 41 Copynumber: 6.6 Consensus size: 41
1511472 ACGTTATTTG
* *
1511482 GGCTCTGTGCCTAGCAGGCTTTGTGTCGGTG-A-TAT-TCG
1 GGCTTTGTGCCTAGCAGGCTTTGTGTCGGTGTATTATATCA
* * * **
1511520 GGCTCTGTACGTAGCAGGCTTCATGTCGGTGTATTATATCA
1 GGCTTTGTGCCTAGCAGGCTTTGTGTCGGTGTATTATATCA
* * * * * *
1511561 GGCTTTATGCGTAGCAGGATTTTGTGTCGATGTTTTATATCG
1 GGCTTTGTGCCTAGCAGG-CTTTGTGTCGGTGTATTATATCA
** * **
1511603 GGC--TGTGCCTAGCAGGCTTCATGCCAATGTATTATATCA
1 GGCTTTGTGCCTAGCAGGCTTTGTGTCGGTGTATTATATCA
*
1511642 GGCTTTGTGCCTAGTAGGCTTTGTG-CTGGTGTATTATATCA
1 GGCTTTGTGCCTAGCAGGCTTTGTGTC-GGTGTATTATATCA
* * *
1511683 GGCTTTGGGCCTAGTAGGCTTCGTGTCGGTGTATTATATCA
1 GGCTTTGTGCCTAGCAGGCTTTGTGTCGGTGTATTATATCA
* * *
1511724 GACTTTGTGCCTAGTAAGCTTTGTGT
1 GGCTTTGTGCCTAGCAGGCTTTGTGT
1511750 TGGTATGTTA
Statistics
Matches: 188, Mismatches: 34, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
38 27 0.14
39 20 0.11
40 15 0.08
41 105 0.56
42 21 0.11
ACGTcount: A:0.16, C:0.18, G:0.29, T:0.37
Consensus pattern (41 bp):
GGCTTTGTGCCTAGCAGGCTTTGTGTCGGTGTATTATATCA
Found at i:1511777 original size:41 final size:40
Alignment explanation
Indices: 1511630--1511777 Score: 161
Period size: 41 Copynumber: 3.6 Consensus size: 40
1511620 TTCATGCCAA
* *
1511630 TGTATTATATCAGGCTTTGTGCCTAGTAGGCTTTGTGCTGG
1 TGTATTATATCA-GCTTTGAGCCTAGTAGGCTTTGTGTTGG
* * *
1511671 TGTATTATATCAGGCTTTGGGCCTAGTAGGCTTCGTGTCGG
1 TGTATTATATCA-GCTTTGAGCCTAGTAGGCTTTGTGTTGG
* *
1511712 TGTATTATATCAGACTTTGTGCCTAGTAAGCTTTGTGTTGG
1 TGTATTATATCAG-CTTTGAGCCTAGTAGGCTTTGTGTTGG
* * * *
1511753 TATGTTATATTATGCTTCGAGCCTA
1 TGTATTATATCA-GCTTTGAGCCTA
1511778 CCGTCTTCGT
Statistics
Matches: 92, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
40 1 0.01
41 90 0.98
42 1 0.01
ACGTcount: A:0.18, C:0.15, G:0.26, T:0.41
Consensus pattern (40 bp):
TGTATTATATCAGCTTTGAGCCTAGTAGGCTTTGTGTTGG
Found at i:1512446 original size:15 final size:17
Alignment explanation
Indices: 1512416--1512457 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1512406 CGTACAATGG
1512416 CATCAA-TCATGCAATA
1 CATCAATTCATGCAATA
1512432 C-TCAATTCATG-AATA
1 CATCAATTCATGCAATA
*
1512447 CATCATTTCAT
1 CATCAATTCAT
1512458 ACCTTACTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.33
Consensus pattern (17 bp):
CATCAATTCATGCAATA
Found at i:1518298 original size:14 final size:13
Alignment explanation
Indices: 1518279--1518312 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
1518269 AATTTTCTCA
1518279 TTTCTTTTTCTTTC
1 TTTCTTTTTC-TTC
1518293 TTTCTTTTTCTTC
1 TTTCTTTTTCTTC
1518306 TTTCTTT
1 TTTCTTT
1518313 CCCCTGTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTCTTTTTCTTC
Found at i:1519217 original size:21 final size:22
Alignment explanation
Indices: 1519190--1519240 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
1519180 TATATGTGAG
1519190 AAATTTACT-TAAGTTATGGAT
1 AAATTTACTCTAAGTTATGGAT
* *
1519211 GAATTTA-TCTAGGTTATGGAT
1 AAATTTACTCTAAGTTATGGAT
*
1519232 AAATATACT
1 AAATTTACT
1519241 AATTTGTGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.04
21 22 0.92
22 1 0.04
ACGTcount: A:0.37, C:0.06, G:0.16, T:0.41
Consensus pattern (22 bp):
AAATTTACTCTAAGTTATGGAT
Found at i:1523786 original size:40 final size:40
Alignment explanation
Indices: 1523721--1523931 Score: 266
Period size: 40 Copynumber: 5.3 Consensus size: 40
1523711 TCTTCGGAAT
* * * *
1523721 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
* * * * *
1523760 TTAACCCGGGT-ATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTC
* *
1523800 TTAGCCCGGAT-ATATCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTC
1523840 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
* *
1523880 TTAACCCGGATAAAATCACTAGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
1523920 TTAGCCCGGATA
1 TTAGCCCGGATA
1523932 TCATTCAAAT
Statistics
Matches: 153, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
39 5 0.03
40 144 0.94
41 4 0.03
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (40 bp):
TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
Found at i:1531545 original size:14 final size:14
Alignment explanation
Indices: 1531526--1531556 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1531516 TATCTAAACT
1531526 ATTGGATTAGCGGC
1 ATTGGATTAGCGGC
*
1531540 ATTGGATTAGTGGC
1 ATTGGATTAGCGGC
1531554 ATT
1 ATT
1531557 ATAATTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.10, G:0.32, T:0.35
Consensus pattern (14 bp):
ATTGGATTAGCGGC
Found at i:1535164 original size:38 final size:38
Alignment explanation
Indices: 1535105--1535241 Score: 150
Period size: 38 Copynumber: 3.6 Consensus size: 38
1535095 AACATAATAT
*
1535105 TATTCAGGCT-TCGTGCCTAGCAGACTTTGTGCCGGTGA
1 TATTCAGGCTCT-GTACCTAGCAGACTTTGTGCCGGTGA
* * * * *
1535143 TATTCGGGCGCTGTACTTAGCAGCCTTTGTGCCGATGA
1 TATTCAGGCTCTGTACCTAGCAGACTTTGTGCCGGTGA
** * *
1535181 TATTTTGGCTCTGTACCTAGCAGGCTTTGTGCCAGTGA
1 TATTCAGGCTCTGTACCTAGCAGACTTTGTGCCGGTGA
* *
1535219 TATTCAGGCTCTGTGCGTAGCAG
1 TATTCAGGCTCTGTACCTAGCAG
1535242 GCTTCCTACC
Statistics
Matches: 81, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
38 80 0.99
39 1 0.01
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (38 bp):
TATTCAGGCTCTGTACCTAGCAGACTTTGTGCCGGTGA
Found at i:1535285 original size:41 final size:41
Alignment explanation
Indices: 1535102--1535455 Score: 261
Period size: 41 Copynumber: 8.9 Consensus size: 41
1535092 AGAAACATAA
* *
1535102 TATTAT-TCAGGCT-TCGTGCCTAGCAGACTTTGTGCCGGTG
1 TATTATATCAGGCTCT-GTGCCTAGCAGGCTTTGTGCCAGTG
* * * * *
1535142 -A-TAT-TCGGGCGCTGTACTTAGCAGCCTTTGTGCC-GATG
1 TATTATATCAGGCTCTGTGCCTAGCAGGCTTTGTGCCAG-TG
*
1535180 ATATT-T-T--GGCTCTGTACCTAGCAGGCTTTGTGCCAGTG
1 -TATTATATCAGGCTCTGTGCCTAGCAGGCTTTGTGCCAGTG
* ** *
1535218 -A-TAT-TCAGGCTCTGTGCGTAGCAGGCTTCCTACCAGTG
1 TATTATATCAGGCTCTGTGCCTAGCAGGCTTTGTGCCAGTG
* * * *
1535256 TATTACATCAGGCTTTGTGCCTAGTAGGCTTTATGCCAGTG
1 TATTATATCAGGCTCTGTGCCTAGCAGGCTTTGTGCCAGTG
** * * *
1535297 TATTATATTGGGCTCTGTGCCTAGCAAGCTTCGTGTC-GATG
1 TATTATATCAGGCTCTGTGCCTAGCAGGCTTTGTGCCAG-TG
* **
1535338 TATTATATCAGGCTTTGTGCCTCA-CAGGCTTTGTGCTGGTG
1 TATTATATCAGGCTCTGTGCCT-AGCAGGCTTTGTGCCAGTG
* * * * * * * *
1535379 TATTATATTAGGTTTTGTGTCTAGTAAGCTTTGTGTCAATG
1 TATTATATCAGGCTCTGTGCCTAGCAGGCTTTGTGCCAGTG
*
1535420 TATTATATCAGGCTCTGTGCCTAGTAGGCTTTGTGC
1 TATTATATCAGGCTCTGTGCCTAGCAGGCTTTGTGC
1535456 TGGTATGTTA
Statistics
Matches: 247, Mismatches: 51, Indels: 31
0.75 0.16 0.09
Matches are distributed among these distances:
35 1 0.00
36 3 0.01
37 1 0.00
38 80 0.32
39 4 0.02
40 7 0.03
41 149 0.60
42 2 0.01
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (41 bp):
TATTATATCAGGCTCTGTGCCTAGCAGGCTTTGTGCCAGTG
Found at i:1535452 original size:82 final size:82
Alignment explanation
Indices: 1535218--1535470 Score: 292
Period size: 82 Copynumber: 3.1 Consensus size: 82
1535208 TGTGCCAGTG
* * * ** * *
1535218 ATATTCAGGCTCTGTGCGTAGCAGGCTTCCTACCAGTGTATTACATCAGGCTTTGTGCCTAGTAG
1 ATATT-AGGCTCTGTGCCTAGCAAGCTTCGTGTCAATGTATTATATCAGGCTTTGTGCCTAGTAG
* **
1535283 GCTTTATGCCAGTGTATT
65 GCTTTGTGCTGGTGTATT
* * *
1535301 ATATTGGGCTCTGTGCCTAGCAAGCTTCGTGTCGATGTATTATATCAGGCTTTGTGCCTCA-CAG
1 ATATTAGGCTCTGTGCCTAGCAAGCTTCGTGTCAATGTATTATATCAGGCTTTGTGCCT-AGTAG
1535365 GCTTTGTGCTGGTGTATT
65 GCTTTGTGCTGGTGTATT
* * * * * *
1535383 ATATTAGGTTTTGTGTCTAGTAAGCTTTGTGTCAATGTATTATATCAGGCTCTGTGCCTAGTAGG
1 ATATTAGGCTCTGTGCCTAGCAAGCTTCGTGTCAATGTATTATATCAGGCTTTGTGCCTAGTAGG
* *
1535448 CTTTGTGCTGGTATGTT
66 CTTTGTGCTGGTGTATT
1535465 ATATTA
1 ATATTA
1535471 AGCTTCGAGC
Statistics
Matches: 144, Mismatches: 24, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
81 1 0.01
82 137 0.95
83 6 0.04
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (82 bp):
ATATTAGGCTCTGTGCCTAGCAAGCTTCGTGTCAATGTATTATATCAGGCTTTGTGCCTAGTAGG
CTTTGTGCTGGTGTATT
Found at i:1535970 original size:21 final size:19
Alignment explanation
Indices: 1535927--1535970 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
1535917 AGTTAAAGGG
*
1535927 TTTACTTATATATGATAAA
1 TTTACTTAAATATGATAAA
*
1535946 TTTACTTAAATTATGGATGAA
1 TTTACTTAAA-TAT-GATAAA
1535967 TTTA
1 TTTA
1535971 TCTGGGTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 9 0.43
20 3 0.14
21 9 0.43
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.48
Consensus pattern (19 bp):
TTTACTTAAATATGATAAA
Found at i:1537936 original size:21 final size:22
Alignment explanation
Indices: 1537911--1537966 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
1537901 AGACGAAGTC
**
1537911 GAAGGATCAAATGACTTCACCA
1 GAAGGATCAAATGACGACACCA
* *
1537933 -AAGGACCAAAGGACGACACCA
1 GAAGGATCAAATGACGACACCA
1537954 GAAGG-TCAAATGA
1 GAAGGATCAAATGA
1537967 TGATACTGGA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (22 bp):
GAAGGATCAAATGACGACACCA
Found at i:1539065 original size:24 final size:24
Alignment explanation
Indices: 1539038--1539087 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1539028 TTGAAAAGAA
1539038 AGCTTAATTGATTGAGAACTTAAT
1 AGCTTAATTGATTGAGAACTTAAT
1539062 AGCTTAATTGATTGAGAACTTAAT
1 AGCTTAATTGATTGAGAACTTAAT
1539086 AG
1 AG
1539088 GAGAATTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (24 bp):
AGCTTAATTGATTGAGAACTTAAT
Found at i:1539094 original size:24 final size:24
Alignment explanation
Indices: 1539043--1539094 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1539033 AAGAAAGCTT
**
1539043 AATTGATTGAGAACTTAATAGCTT
1 AATTGATTGAGAACTTAATAGCAG
*
1539067 AATTGATTGAGAACTTAATAGGAG
1 AATTGATTGAGAACTTAATAGCAG
1539091 AATT
1 AATT
1539095 TATACACATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (24 bp):
AATTGATTGAGAACTTAATAGCAG
Found at i:1546344 original size:20 final size:21
Alignment explanation
Indices: 1546310--1546348 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1546300 TTAATTTTTC
*
1546310 TATTTTTAATGATAATTAATT
1 TATTTTTAATAATAATTAATT
1546331 TATTTTTAA-AATAATTAA
1 TATTTTTAATAATAATTAA
1546349 ACTGTGGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (21 bp):
TATTTTTAATAATAATTAATT
Found at i:1554877 original size:62 final size:62
Alignment explanation
Indices: 1554780--1554904 Score: 241
Period size: 62 Copynumber: 2.0 Consensus size: 62
1554770 AACATTTGAG
1554780 TATGGCATGCTAAATGATTCAATGCAATAATCCTACCCATTCATCCGCTACACACCACGAGT
1 TATGGCATGCTAAATGATTCAATGCAATAATCCTACCCATTCATCCGCTACACACCACGAGT
*
1554842 TATGGCATGCTAAATGATTCAATGCAATAATCCTACCCATTCATCCGCTACACGCCACGAGT
1 TATGGCATGCTAAATGATTCAATGCAATAATCCTACCCATTCATCCGCTACACACCACGAGT
1554904 T
1 T
1554905 TCTAAAATAG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (62 bp):
TATGGCATGCTAAATGATTCAATGCAATAATCCTACCCATTCATCCGCTACACACCACGAGT
Found at i:1555697 original size:17 final size:16
Alignment explanation
Indices: 1555644--1555715 Score: 60
Period size: 17 Copynumber: 4.4 Consensus size: 16
1555634 TTATCACTCT
*
1555644 AATATTAAATTAATAA
1 AATATTAAATTAATTA
*
1555660 AATACT--ATTAATATA
1 AATATTAAATTAAT-TA
*
1555675 AGTATTAAATTAAATTA
1 AATATTAAATT-AATTA
1555692 AATATTAAATCT-ATTAA
1 AATATTAAAT-TAATT-A
1555709 AATATTA
1 AATATTA
1555716 TCATTATTGG
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
14 6 0.13
15 5 0.11
16 8 0.18
17 22 0.49
18 4 0.09
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (16 bp):
AATATTAAATTAATTA
Found at i:1558988 original size:60 final size:59
Alignment explanation
Indices: 1558908--1559047 Score: 169
Period size: 60 Copynumber: 2.3 Consensus size: 59
1558898 TTTAGTGTTA
*
1558908 ACTGAGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCT-TAC-AGTAAC-AGAGTAT
1 ACTGGGCC-TAGCCCATATCAATATTAATCTGGGCCATAG-CCCTATACAAGT--CGAGA-TAT
* *
1558969 ACTGGGCCTAGCCCATATCAGTATTAATCTGGGCCGTAGCCCTATACAAGTCGAGATAT
1 ACTGGGCCTAGCCCATATCAATATTAATCTGGGCCATAGCCCTATACAAGTCGAGATAT
* *
1559028 ATTGGGCCTTGCCCATATCA
1 ACTGGGCCTAGCCCATATCA
1559048 GCACAGTTGG
Statistics
Matches: 71, Mismatches: 5, Indels: 8
0.85 0.06 0.10
Matches are distributed among these distances:
59 26 0.37
60 35 0.49
61 10 0.14
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.26
Consensus pattern (59 bp):
ACTGGGCCTAGCCCATATCAATATTAATCTGGGCCATAGCCCTATACAAGTCGAGATAT
Found at i:1559987 original size:29 final size:30
Alignment explanation
Indices: 1559940--1560007 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
1559930 TGGCCCAAGA
* *
1559940 GTAAATACTCAAAATTTGAAGGATTAA-AGT
1 GTAAATA-TCAAAAGTTGAAGGACTAATAGT
*
1559970 GTAAATATGAAAAGTTGAAGGACTAATAGT
1 GTAAATATCAAAAGTTGAAGGACTAATAGT
*
1560000 GCAAATAT
1 GTAAATAT
1560008 TTTAAGGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (30 bp):
GTAAATATCAAAAGTTGAAGGACTAATAGT
Found at i:1560285 original size:7 final size:8
Alignment explanation
Indices: 1560269--1560299 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
1560259 TTTTTAAATG
1560269 TTATTTTT
1 TTATTTTT
1560277 TTATTTTTT
1 TTA-TTTTT
1560286 TTATTTTT
1 TTATTTTT
1560294 TTATTT
1 TTATTT
1560300 AATATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (8 bp):
TTATTTTT
Found at i:1562490 original size:46 final size:46
Alignment explanation
Indices: 1562433--1562660 Score: 341
Period size: 46 Copynumber: 5.0 Consensus size: 46
1562423 AGTGTGCTCT
* *
1562433 CTGAAATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
1562479 CTGATATGAAATGTGTAAGATCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
1562525 CTGATATGAAATGTGTAAGACCATGGGTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1562571 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
1562617 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
1562661 TCATGTCAAA
Statistics
Matches: 167, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 1 0.01
46 166 0.99
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:1566138 original size:96 final size:96
Alignment explanation
Indices: 1565974--1566169 Score: 295
Period size: 96 Copynumber: 2.0 Consensus size: 96
1565964 ATCATACATA
* * *
1565974 ATAACATATTCAAATATCACATGTCCTCATCTAACACAGCAACACAGAAATGAATCATCAAAATT
1 ATAACATATTCAAATATCACATGTCCTCATCCAAAACAGCAACACAGAAATGAATCATAAAAATT
*
1566039 AACAAAGCATGGAT-TAGCCTGAATAAATCAC
66 AACAAAGCATAGATCTA-CCTGAATAAATCAC
* * *
1566070 ATAACATATTCAGATATCACATGTCTTCATCCAAAATAGCAACACAGAAATGAATCATAAAAATT
1 ATAACATATTCAAATATCACATGTCCTCATCCAAAACAGCAACACAGAAATGAATCATAAAAATT
*
1566135 AACAGAGCATAGATCCTACCTGAATAAATCAC
66 AACAAAGCATAGAT-CTACCTGAATAAATCAC
1566167 ATA
1 ATA
1566170 CCTTAAACAC
Statistics
Matches: 90, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
96 71 0.79
97 17 0.19
98 2 0.02
ACGTcount: A:0.46, C:0.21, G:0.09, T:0.23
Consensus pattern (96 bp):
ATAACATATTCAAATATCACATGTCCTCATCCAAAACAGCAACACAGAAATGAATCATAAAAATT
AACAAAGCATAGATCTACCTGAATAAATCAC
Found at i:1572383 original size:28 final size:28
Alignment explanation
Indices: 1572351--1572415 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
1572341 ATTTACTAGA
*
1572351 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* *
1572379 ATACCCCTATGTATGCTAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
1572407 ATACCCCTA
1 ATACCCCTA
1572416 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:1572581 original size:29 final size:29
Alignment explanation
Indices: 1572521--1572608 Score: 94
Period size: 28 Copynumber: 3.1 Consensus size: 29
1572511 AGGAAGCGTC
*
1572521 CTGGTGGCTA-TGCCACAAATTATCTGT-T
1 CTGGTGGC-ACTGCCACAAAATATCTGTAT
1572549 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAAATATCTGTAT
* * * *
1572578 CTGGTGACTCTGTCAC-ATAT-TCTGTAT
1 CTGGTGGCACTGCCACAAAATATCTGTAT
1572605 CTGG
1 CTGG
1572609 AAGCCATGCT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
27 12 0.23
28 27 0.51
29 14 0.26
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.34
Consensus pattern (29 bp):
CTGGTGGCACTGCCACAAAATATCTGTAT
Found at i:1573071 original size:19 final size:19
Alignment explanation
Indices: 1573047--1573085 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1573037 TTTTAATTAT
* *
1573047 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
1573066 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
1573085 T
1 T
1573086 ATGATGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:1573697 original size:11 final size:10
Alignment explanation
Indices: 1573669--1573702 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
1573659 AGCCTGTAAG
1573669 TATTCTGAAT
1 TATTCTGAAT
*
1573679 TTTTCTGAAT
1 TATTCTGAAT
1573689 ATATTCTGAAT
1 -TATTCTGAAT
1573700 TAT
1 TAT
1573703 CTGTCTATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (10 bp):
TATTCTGAAT
Found at i:1579840 original size:28 final size:28
Alignment explanation
Indices: 1579808--1579872 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
1579798 ATTTACTAGA
*
1579808 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* *
1579836 ATACCCCTATGTATGCTAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
1579864 ATACCCCTA
1 ATACCCCTA
1579873 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:1580019 original size:28 final size:29
Alignment explanation
Indices: 1579978--1580040 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 29
1579968 AGGAAGCGTC
*
1579978 CTGGTGGCTATGCCACAAATTATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTAT
1580006 CTGGTGGC-ACTGCCACAAAATATCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGTAT
1580035 CTGGTG
1 CTGGTG
1580041 ACTCTGTCAC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
27 1 0.03
28 24 0.75
29 7 0.22
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (29 bp):
CTGGTGGCTATGCCACAAAATATCTGTAT
Found at i:1580051 original size:29 final size:28
Alignment explanation
Indices: 1579988--1580051 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
1579978 CTGGTGGCTA
* *
1579988 TGCCACAAATTATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
1580016 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
1580045 TGTCACA
1 TGCCACA
1580052 TTTTCTGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 16 0.52
29 15 0.48
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:1583165 original size:21 final size:21
Alignment explanation
Indices: 1583083--1583192 Score: 89
Period size: 21 Copynumber: 5.2 Consensus size: 21
1583073 ACTCATAAGA
1583083 GTTTCCGTTCAA-TCTTAATGG
1 GTTTCCGTTCAACTCTT-ATGG
* * * *
1583104 GATTCCGTTCAGCTCTTTTGA
1 GTTTCCGTTCAACTCTTATGG
* ** * *
1583125 GCTTCTATTTAACCCTTATGG
1 GTTTCCGTTCAACTCTTATGG
*
1583146 GTTTCCGTTCAACTCTTATGA
1 GTTTCCGTTCAACTCTTATGG
*
1583167 GCTTCCGTTCAA-TCCTTATGG
1 GTTTCCGTTCAACT-CTTATGG
1583188 GTTTC
1 GTTTC
1583193 TGTTTAGCAC
Statistics
Matches: 66, Mismatches: 21, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
20 1 0.02
21 61 0.92
22 4 0.06
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.43
Consensus pattern (21 bp):
GTTTCCGTTCAACTCTTATGG
Found at i:1583205 original size:21 final size:21
Alignment explanation
Indices: 1583181--1583233 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1583171 CCGTTCAATC
*
1583181 CTTATGGGTTTCTGTTTAGCA
1 CTTATGGGCTTCTGTTTAGCA
*
1583202 CTTATGTGCTTCTGTTTAGC-
1 CTTATGGGCTTCTGTTTAGCA
*
1583222 CTT-CGGGCTTCT
1 CTTATGGGCTTCT
1583234 AAAAACGATG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 7 0.25
20 3 0.11
21 18 0.64
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (21 bp):
CTTATGGGCTTCTGTTTAGCA
Found at i:1583207 original size:42 final size:42
Alignment explanation
Indices: 1583062--1583192 Score: 138
Period size: 42 Copynumber: 3.1 Consensus size: 42
1583052 GCTCTCACAA
* * * * *
1583062 GTTTCTGTTTAACTCATAAGAGTTTCCGTTCAAT-CTTAATGG
1 GTTTCCGTTCAACTCTTATGAGCTTCCGTTCAATCCTT-ATGG
* * * ** * *
1583104 GATTCCGTTCAGCTCTTTTGAGCTTCTATTTAACCCTTATGG
1 GTTTCCGTTCAACTCTTATGAGCTTCCGTTCAATCCTTATGG
1583146 GTTTCCGTTCAACTCTTATGAGCTTCCGTTCAATCCTTATGG
1 GTTTCCGTTCAACTCTTATGAGCTTCCGTTCAATCCTTATGG
1583188 GTTTC
1 GTTTC
1583193 TGTTTAGCAC
Statistics
Matches: 69, Mismatches: 19, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
42 66 0.96
43 3 0.04
ACGTcount: A:0.18, C:0.22, G:0.17, T:0.43
Consensus pattern (42 bp):
GTTTCCGTTCAACTCTTATGAGCTTCCGTTCAATCCTTATGG
Found at i:1583213 original size:42 final size:42
Alignment explanation
Indices: 1583085--1583213 Score: 143
Period size: 42 Copynumber: 3.1 Consensus size: 42
1583075 TCATAAGAGT
* *
1583085 TTCCGTTCAAT-CTTAATGGGATTCCGTTCAGCTCTTTTGAGC
1 TTCCGTTCAATCCTT-ATGGGTTTCCGTTCAGCTCTTATGAGC
** * * *
1583127 TTCTATTTAACCCTTATGGGTTTCCGTTCAACTCTTATGAGC
1 TTCCGTTCAATCCTTATGGGTTTCCGTTCAGCTCTTATGAGC
* * * *
1583169 TTCCGTTCAATCCTTATGGGTTTCTGTTTAGCACTTATGTGC
1 TTCCGTTCAATCCTTATGGGTTTCCGTTCAGCTCTTATGAGC
1583211 TTC
1 TTC
1583214 TGTTTAGCCT
Statistics
Matches: 70, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
42 67 0.96
43 3 0.04
ACGTcount: A:0.16, C:0.23, G:0.17, T:0.43
Consensus pattern (42 bp):
TTCCGTTCAATCCTTATGGGTTTCCGTTCAGCTCTTATGAGC
Found at i:1584683 original size:23 final size:23
Alignment explanation
Indices: 1584654--1584700 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1584644 ATTATAATTG
1584654 ATTATTCTTTAAGGAAAACAAAT
1 ATTATTCTTTAAGGAAAACAAAT
1584677 ATTATTCTTTAAGGAAAACAAAT
1 ATTATTCTTTAAGGAAAACAAAT
1584700 A
1 A
1584701 GATTACATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.34
Consensus pattern (23 bp):
ATTATTCTTTAAGGAAAACAAAT
Found at i:1586364 original size:18 final size:18
Alignment explanation
Indices: 1586341--1586376 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1586331 CAAACTCCAG
*
1586341 CAAACTCTAGCAAGGAAC
1 CAAACTCCAGCAAGGAAC
1586359 CAAACTCCAGCAAGGAAC
1 CAAACTCCAGCAAGGAAC
1586377 AACAAGAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.31, G:0.17, T:0.08
Consensus pattern (18 bp):
CAAACTCCAGCAAGGAAC
Found at i:1591826 original size:17 final size:18
Alignment explanation
Indices: 1591800--1591833 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1591790 ACTTTTTGGG
*
1591800 TTTTCTTTTTAGATTTTT
1 TTTTCTTTTTAAATTTTT
1591818 TTTTC-TTTTAAATTTT
1 TTTTCTTTTTAAATTTT
1591834 AGTGGTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (18 bp):
TTTTCTTTTTAAATTTTT
Found at i:1594108 original size:15 final size:17
Alignment explanation
Indices: 1594074--1594110 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
1594064 TTTTTTACTG
*
1594074 TATATTATTATAATTTT
1 TATATTATTATAAATTT
1594091 TATATT-TTA-AAATTT
1 TATATTATTATAAATTT
1594106 TATAT
1 TATAT
1594111 AATTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 10 0.53
16 3 0.16
17 6 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATTATTATAAATTT
Found at i:1594117 original size:18 final size:16
Alignment explanation
Indices: 1594074--1594120 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
1594064 TTTTTTACTG
*
1594074 TATATTATTATAATTTT
1 TATATT-TTAAAATTTT
1594091 TATATTTTAAAATTTT
1 TATATTTTAAAATTTT
1594107 ATATAATTTTAAAA
1 -TAT-ATTTTAAAA
1594121 AATCATCATC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 9 0.33
17 9 0.33
18 9 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATTTTAAAATTTT
Found at i:1595751 original size:22 final size:22
Alignment explanation
Indices: 1595723--1595765 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1595713 ACATACACAG
1595723 AGAGTGGGCTCCTATAAAAAAC
1 AGAGTGGGCTCCTATAAAAAAC
1595745 AGAGTGGGCTCCTATAAAAAA
1 AGAGTGGGCTCCTATAAAAAA
1595766 TTGTAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.19
Consensus pattern (22 bp):
AGAGTGGGCTCCTATAAAAAAC
Found at i:1603664 original size:26 final size:26
Alignment explanation
Indices: 1603628--1603711 Score: 132
Period size: 26 Copynumber: 3.2 Consensus size: 26
1603618 CATGAAATTC
*
1603628 TTATCATGAAACATTTGCCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
1603654 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
1603680 TTATCATGGAACATTTACCAAACCTA
1 TTATCATGAAACATTTACCTAACCCA
1603706 TTATCA
1 TTATCA
1603712 ATTTATATCA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.32
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:1606594 original size:27 final size:27
Alignment explanation
Indices: 1606519--1606620 Score: 116
Period size: 27 Copynumber: 3.8 Consensus size: 27
1606509 AAGGCAAACC
*
1606519 ATACAGAGTATACCACAAAGGCCATAT
1 ATACAGAGTATACCACAAAGGTCATAT
* * * *
1606546 ATATAAAGTATGCCACAAAGGTTATAT
1 ATACAGAGTATACCACAAAGGTCATAT
*
1606573 ATACAGAGTATACCACAAAGGTGAT-T
1 ATACAGAGTATACCACAAAGGTCATAT
* *
1606599 CATTCAGAGTACACCACAAAGG
1 -ATACAGAGTATACCACAAAGG
1606621 CTGATAGGAT
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
26 1 0.02
27 62 0.98
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.22
Consensus pattern (27 bp):
ATACAGAGTATACCACAAAGGTCATAT
Found at i:1610011 original size:31 final size:31
Alignment explanation
Indices: 1609973--1610037 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
1609963 GAGTGATGGA
*
1609973 TGAGAAATTGATACTCAAAGTAAGCCACTTG
1 TGAGAAATTGATACTCAAAATAAGCCACTTG
*
1610004 TGAGAAATTGATACTCAAAATAAGCTACTTG
1 TGAGAAATTGATACTCAAAATAAGCCACTTG
1610035 TGA
1 TGA
1610038 ATTATGTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (31 bp):
TGAGAAATTGATACTCAAAATAAGCCACTTG
Found at i:1610693 original size:64 final size:65
Alignment explanation
Indices: 1610591--1610720 Score: 208
Period size: 64 Copynumber: 2.0 Consensus size: 65
1610581 GTCCGATAAA
* * *
1610591 CATTGGACTGTCATTGCACATTCCCCATAACGCTCGTTAACC-AAACCGCTTGGGTCCAAATCAT
1 CATTGGACTGTCATTGCACACTCCCCATAACGCGCGTTAACCAAAACAGCTTGGGTCCAAATCAT
* *
1610655 CATTGGGCTGTCATTGCACACTCCCCCTAACGCGCGTTAACCAAAACAGCTTGGGTCCAAATCAT
1 CATTGGACTGTCATTGCACACTCCCCATAACGCGCGTTAACCAAAACAGCTTGGGTCCAAATCAT
1610720 C
1 C
1610721 TGATAGTTTC
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
64 38 0.63
65 22 0.37
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.25
Consensus pattern (65 bp):
CATTGGACTGTCATTGCACACTCCCCATAACGCGCGTTAACCAAAACAGCTTGGGTCCAAATCAT
Found at i:1612201 original size:27 final size:27
Alignment explanation
Indices: 1612171--1612226 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1612161 AACTTGTTAC
1612171 TGATATGTATATCTTTATCATTGATCT
1 TGATATGTATATCTTTATCATTGATCT
1612198 TGATATGTATATCTTTATCATTGATCT
1 TGATATGTATATCTTTATCATTGATCT
1612225 TG
1 TG
1612227 TAGGTTCTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.25, C:0.11, G:0.12, T:0.52
Consensus pattern (27 bp):
TGATATGTATATCTTTATCATTGATCT
Found at i:1616276 original size:5 final size:5
Alignment explanation
Indices: 1616266--1616290 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1616256 CAATCTCATG
1616266 CTCTT CTCTT CTCTT CTCTT CTCTT
1 CTCTT CTCTT CTCTT CTCTT CTCTT
1616291 TGTTTTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
CTCTT
Found at i:1630708 original size:502 final size:500
Alignment explanation
Indices: 1629240--1631250 Score: 3791
Period size: 502 Copynumber: 4.0 Consensus size: 500
1629230 AATATGTTAT
* * * * *
1629240 AATATTTTAGTCACTGAGTTGTAAATTGCCGTTAACGGTTTAAGGGTAAGCTAACATGGCACATT
1 AATATTATAGTCACTGGGTTGTAAATTGCCATTAACGGTTTAAGGGTAAGCTAACGTGGCACGTT
* *
1629305 AAATCATCATTTCAAACAAAAATTTTAACTTAAAGTATACAATTGATCCTCATATTTTTTTTGTT
66 AAATTATCATTTCAAACAAAAATTTTAAGTTAAAGTATACAATTGATCCTCATATTTTTTTTGTT
1629370 TTGAGTAATCTATTTTTTTCTTTTATATTCTTTTAACTTTCCTTTTTTTTTCTTTTTTTTCCATT
131 TTGAGTAATCTATTTTTTTCTTTTATATTCTTTTAACTTTCCTTTTTTTTTCTTTTTTTTCCATT
* * *
1629435 CTCCCTCTGTTTTCATCCCCTTCCTCTCTCTCTCTTTTAACGTAGTTTTTCTATATTTTTCATTT
196 CTCCCTCTATTTTCATCCCCTCCCTCTCTCTCTCTTTTAACGTAGTTTTTCTATATTTTCCATTT
1629500 GTTAAAACTATTTTATGTTTATGAAAAAAGAAAAGGCGAACGTTGAAACCAAAATAACACTTGCT
261 GTTAAAACTATTTTATGTTTATGAAAAAAGAAAAGGCGAACGTTGAAACCAAAATAACACTTGCT
* *
1629565 TCGTGAGGGTGTGCCTCATATTTACGAGACGGCGTCCTGATGACGTGACAAACGACGTCCAAACG
326 TCGTGAGGGTGTGCCTCATATTTACGAGACGGCGTCGTGATGACGTGACAAACGACGTCCCAACG
1629630 AGAGG-----AA-GTCGCGACGTGGTGACGTGTTCCCAAATTCAATTGGGTTTTCTTCTCCTAGT
391 AGAGGAAAACAATGTCGCGACGTGGTGACGTGTTCCCAAATTCAATTGGGTTTTCTTCTCCTAGT
1629689 TAAACTCTACTATTTATTCTTTAATTAAACTCTGATTATTCTAGG
456 TAAACTCTACTATTTATTCTTTAATTAAACTCTGATTATTCTAGG
1629734 AATATTATAGTCACTGGGTTGTAAATTGCCATTAACGGTTTAAGGGTAAGCTAACGTGGCACGTT
1 AATATTATAGTCACTGGGTTGTAAATTGCCATTAACGGTTTAAGGGTAAGCTAACGTGGCACGTT
1629799 AAATTATCATTTCAAACAAAAATTTTAAGTTAAAGTATACAATTGATCCTCATATTTTTTTTGTT
66 AAATTATCATTTCAAACAAAAATTTTAAGTTAAAGTATACAATTGATCCTCATATTTTTTTTGTT
1629864 TTGAGTAATCTATTTTTTTCTTTTATATTCTTTTAACTTTCCTTTTTTTTTCTTTTTTTTCCATT
131 TTGAGTAATCTATTTTTTTCTTTTATATTCTTTTAACTTTCCTTTTTTTTTCTTTTTTTTCCATT
* * *
1629929 CTCCCTCTGTTTTCATCCCCTTCCTCTCTCTCTCTTTTAACGTAGTTTTTCTATATTTTTCATTT
196 CTCCCTCTATTTTCATCCCCTCCCTCTCTCTCTCTTTTAACGTAGTTTTTCTATATTTTCCATTT
1629994 GTTAAAACTATTTTATGTTTATGAAAAAAGAAAAGGCGAACGTTGAAACCAAAATAACACTTGCT
261 GTTAAAACTATTTTATGTTTATGAAAAAAGAAAAGGCGAACGTTGAAACCAAAATAACACTTGCT
1630059 TCGTGAGGGTGTGCCTCATATTTACGAGACGGCGTCGTGATGACGTGACAAACGACGTCCCAACG
326 TCGTGAGGGTGTGCCTCATATTTACGAGACGGCGTCGTGATGACGTGACAAACGACGTCCCAACG
1630124 AGAGGAAAACAATGTCGCGACGTGGTGACGTGTTCCCAAATTCAATTGGGTTTTCTTCTCCTAGT
391 AGAGGAAAACAATGTCGCGACGTGGTGACGTGTTCCCAAATTCAATTGGGTTTTCTTCTCCTAGT
1630189 TAAACTCTACTATTTATTCTTTAATTAAACTCTGATTATTCTAGG
456 TAAACTCTACTATTTATTCTTTAATTAAACTCTGATTATTCTAGG
1630234 AATATTATAGTCACTGGGTTGTAAATTGCCATTAACGGTTTAAGGGTAAGCTAACGTGGCACGTT
1 AATATTATAGTCACTGGGTTGTAAATTGCCATTAACGGTTTAAGGGTAAGCTAACGTGGCACGTT
1630299 AAATTATCATTTCAAACAAAAATTTTAAGTTAAAGTATACAATTGATCCTCATATTTTTTTTGTT
66 AAATTATCATTTCAAACAAAAATTTTAAGTTAAAGTATACAATTGATCCTCATATTTTTTTTGTT
1630364 TTGAGTAATCTATTTTTTTCTTTTATATTCTTTTAACTTTCCTTTTTTTTTTCTTTTTTTTTCCA
131 TTGAGTAATCTATTTTTTTCTTTTATATTCTTTTAACTTTCC-TTTTTTTTTC-TTTTTTTTCCA
1630429 TTCTCCCTCTATTTTCATCCCCTCCCTCTCTCTCTCTTTTAACGTAGTTTTTCTATATTTTCCAT
194 TTCTCCCTCTATTTTCATCCCCTCCCTCTCTCTCTCTTTTAACGTAGTTTTTCTATATTTTCCAT
*
1630494 TTGTTAAAACTGTTTTATGTTTATGAAAAAAGAAAAGGCGAACGTTGAAACCAAAATAACACTTG
259 TTGTTAAAACTATTTTATGTTTATGAAAAAAGAAAAGGCGAACGTTGAAACCAAAATAACACTTG
1630559 CTTCGTGAGGGTGTGCCTCATATTTACGAGACGGCGTCGTGATGACGTGACAAACGACGTCCCAA
324 CTTCGTGAGGGTGTGCCTCATATTTACGAGACGGCGTCGTGATGACGTGACAAACGACGTCCCAA
1630624 CGAGAGGAAAACAATGTCGCGACGTGGTGACGTGTTCCCAAATTCAATTGGGTTTTCTTCTCCTA
389 CGAGAGGAAAACAATGTCGCGACGTGGTGACGTGTTCCCAAATTCAATTGGGTTTTCTTCTCCTA
1630689 GTTAAACTCTACTATTTATTCTTTAATTAAACTCTGATTATTCTAGG
454 GTTAAACTCTACTATTTATTCTTTAATTAAACTCTGATTATTCTAGG
1630736 AATATTATAGTCACTGGGTTGTAAATTGCCATTAACGGTTTAAGGGTAAGCTAACGTGGCACGTT
1 AATATTATAGTCACTGGGTTGTAAATTGCCATTAACGGTTTAAGGGTAAGCTAACGTGGCACGTT
1630801 AAATTATCATTTCAAACAAAAATTTTAAGTTAAAGTATACAATTGATCCTCATATTTTTTTTGTT
66 AAATTATCATTTCAAACAAAAATTTTAAGTTAAAGTATACAATTGATCCTCATATTTTTTTTGTT
1630866 TTGAGTAATCTATTTTTTTCTTTTATATTCTTTTAACTTTCCTTTTTTTTTTCTTTTTTTTTCCA
131 TTGAGTAATCTATTTTTTTCTTTTATATTCTTTTAACTTTCC-TTTTTTTTTC-TTTTTTTTCCA
1630931 TTCTCCCTCTATTTTCATCCCCTCCCTCTCTCTCTCTTTTAACGTAGTTTTTCTATATTTTCCAT
194 TTCTCCCTCTATTTTCATCCCCTCCCTCTCTCTCTCTTTTAACGTAGTTTTTCTATATTTTCCAT
*
1630996 TTGTTAAAACTGTTTTATGTTTATGAAAAAAGAAAAGGCGAACGTTGAAACCAAAATAACACTTG
259 TTGTTAAAACTATTTTATGTTTATGAAAAAAGAAAAGGCGAACGTTGAAACCAAAATAACACTTG
1631061 CTTCGTGAGGGTGTGCCTCATATTTACGAGACGGCGTCGTGATGACGTGACAAACGACGTCCCAA
324 CTTCGTGAGGGTGTGCCTCATATTTACGAGACGGCGTCGTGATGACGTGACAAACGACGTCCCAA
1631126 CGAGAGGAAAACAATGTCGCGACGTGGTGACGTGTTCCCAAATTCAATTGGGTTTTCTTCTCCTA
389 CGAGAGGAAAACAATGTCGCGACGTGGTGACGTGTTCCCAAATTCAATTGGGTTTTCTTCTCCTA
1631191 GTTAAACTCTACTATTTATTCTTTAATTAAACTCTGATTATTCTAGG
454 GTTAAACTCTACTATTTATTCTTTAATTAAACTCTGATTATTCTAGG
1631238 AATATTATAGTCA
1 AATATTATAGTCA
1631251 TATTAGGACT
Statistics
Matches: 1496, Mismatches: 13, Indels: 8
0.99 0.01 0.01
Matches are distributed among these distances:
494 386 0.26
499 2 0.00
500 269 0.18
501 10 0.01
502 829 0.55
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.41
Consensus pattern (500 bp):
AATATTATAGTCACTGGGTTGTAAATTGCCATTAACGGTTTAAGGGTAAGCTAACGTGGCACGTT
AAATTATCATTTCAAACAAAAATTTTAAGTTAAAGTATACAATTGATCCTCATATTTTTTTTGTT
TTGAGTAATCTATTTTTTTCTTTTATATTCTTTTAACTTTCCTTTTTTTTTCTTTTTTTTCCATT
CTCCCTCTATTTTCATCCCCTCCCTCTCTCTCTCTTTTAACGTAGTTTTTCTATATTTTCCATTT
GTTAAAACTATTTTATGTTTATGAAAAAAGAAAAGGCGAACGTTGAAACCAAAATAACACTTGCT
TCGTGAGGGTGTGCCTCATATTTACGAGACGGCGTCGTGATGACGTGACAAACGACGTCCCAACG
AGAGGAAAACAATGTCGCGACGTGGTGACGTGTTCCCAAATTCAATTGGGTTTTCTTCTCCTAGT
TAAACTCTACTATTTATTCTTTAATTAAACTCTGATTATTCTAGG
Found at i:1632892 original size:3 final size:3
Alignment explanation
Indices: 1632884--1632922 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1632874 GTGACTATTT
1632884 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1632923 GTTGTCGTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1637802 original size:32 final size:32
Alignment explanation
Indices: 1637753--1637813 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
1637743 TAGCCGTGTG
* *
1637753 GGCCACATGGGCTAGGCCAAGT-TGGGCGTATA
1 GGCCACACGGGCAAGGCCAA-TCTGGGCGTATA
1637785 GGCCACACGGGCAAGGCCAATCTGGGCGT
1 GGCCACACGGGCAAGGCCAATCTGGGCGT
1637814 GTGGACCCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 1 0.04
32 25 0.96
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (32 bp):
GGCCACACGGGCAAGGCCAATCTGGGCGTATA
Found at i:1643098 original size:15 final size:15
Alignment explanation
Indices: 1643074--1643115 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
1643064 TATAGTTTTG
1643074 TTCTGCTCTGCTCTA
1 TTCTGCTCTGCTCTA
* *
1643089 TTCTGTTCTGTTCTA
1 TTCTGCTCTGCTCTA
*
1643104 CTCTGCTCTGCT
1 TTCTGCTCTGCT
1643116 TGATTTGTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.05, C:0.31, G:0.14, T:0.50
Consensus pattern (15 bp):
TTCTGCTCTGCTCTA
Found at i:1645886 original size:15 final size:15
Alignment explanation
Indices: 1645866--1645895 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1645856 CACCCCAATC
1645866 ACAGATACAAAAATA
1 ACAGATACAAAAATA
*
1645881 ACAGATACAATAATA
1 ACAGATACAAAAATA
1645896 TCATGCATAA
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:0.63, C:0.13, G:0.07, T:0.17
Consensus pattern (15 bp):
ACAGATACAAAAATA
Found at i:1655266 original size:20 final size:20
Alignment explanation
Indices: 1655241--1655280 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1655231 ACACTACATC
*
1655241 TCTATTAAGAAAATATGAAA
1 TCTATTAAGAAAATACGAAA
1655261 TCTATTAAGAAAATACGAAA
1 TCTATTAAGAAAATACGAAA
1655281 GAACATTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.55, C:0.07, G:0.10, T:0.28
Consensus pattern (20 bp):
TCTATTAAGAAAATACGAAA
Found at i:1658644 original size:22 final size:22
Alignment explanation
Indices: 1658619--1658714 Score: 122
Period size: 22 Copynumber: 4.3 Consensus size: 22
1658609 GCTAAAACGA
* * *
1658619 TAAGCTCTATCCAGTTTAACAG
1 TAAGCTCTATCGAGCTGAACAG
*
1658641 TAAGCTCTATGGAGCTGAACAG
1 TAAGCTCTATCGAGCTGAACAG
1658663 TAAGCTCTATCGAGCTGAACAG
1 TAAGCTCTATCGAGCTGAACAG
*
1658685 TAAGCTC-ATACGAGCTGAAACGG
1 TAAGCTCTAT-CGAGCTG-AACAG
1658708 TAAGCTC
1 TAAGCTC
1658715 CAATAAGCTG
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
21 2 0.03
22 53 0.80
23 11 0.17
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (22 bp):
TAAGCTCTATCGAGCTGAACAG
Found at i:1658673 original size:44 final size:45
Alignment explanation
Indices: 1658605--1658750 Score: 129
Period size: 44 Copynumber: 3.2 Consensus size: 45
1658595 GTAAGTTTTA
* * *
1658605 ACGAGCTAAAAC-GATAAGCTCTATCCAGTTTAACAGTAAGCTC-T
1 ACGAGCTGAAACAG-TAAGCTCTATCCAGCTGAACAGTAAGCTCAT
* *
1658649 ATGGAGCTG-AACAGTAAGCTCTATCGAGCTGAACAGTAAGCTCAT
1 A-CGAGCTGAAACAGTAAGCTCTATCCAGCTGAACAGTAAGCTCAT
* * *
1658694 ACGAGCTGAAACGGTAAGCTCCAAT-AAGCTGATATATCAGTAAGCTCAT
1 ACGAGCTGAAACAGTAAGCT-CTATCCAGCTG--A-A-CAGTAAGCTCAT
1658743 ACGAGCTG
1 ACGAGCTG
1658751 TGGTGAGTCC
Statistics
Matches: 84, Mismatches: 9, Indels: 13
0.79 0.08 0.12
Matches are distributed among these distances:
44 36 0.43
45 23 0.27
46 3 0.04
47 1 0.01
48 1 0.01
49 20 0.24
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (45 bp):
ACGAGCTGAAACAGTAAGCTCTATCCAGCTGAACAGTAAGCTCAT
Found at i:1660100 original size:43 final size:43
Alignment explanation
Indices: 1660051--1660201 Score: 171
Period size: 43 Copynumber: 3.5 Consensus size: 43
1660041 TATCCCATAT
* * *
1660051 ATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGAA
1 ATGGTCTTACATGTAATCACATATCGATGCCAATGTCCCAGAC
* * * * *
1660094 AGGGTCTTATACGTAATCGA-TTAACGATGCCAATGTCCCAGAC
1 ATGGTCTTACATGTAATC-ACATATCGATGCCAATGTCCCAGAC
* **
1660137 ATGGTCTTACATGTAATCACA-ATACAATGCCAATGTCTTAGAC
1 ATGGTCTTACATGTAATCACATAT-CGATGCCAATGTCCCAGAC
1660180 ATGGTCTTACATGTAATCACAT
1 ATGGTCTTACATGTAATCACAT
1660202 CTCGGTAACC
Statistics
Matches: 88, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
42 2 0.02
43 85 0.97
44 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.30
Consensus pattern (43 bp):
ATGGTCTTACATGTAATCACATATCGATGCCAATGTCCCAGAC
Found at i:1668256 original size:46 final size:46
Alignment explanation
Indices: 1668188--1668313 Score: 116
Period size: 46 Copynumber: 2.7 Consensus size: 46
1668178 ATAACCAAAA
* *
1668188 TTTATAAAAGTTTACAATTTTTTATGATTTTTATAAAAAATT-CTAATT
1 TTTATAAAA-TTTA-AAATTTTTAT-ATTTTTATAAAAAATTAATAATT
* **
1668236 TTTA-ATAAATTTAAAATTTTTA-ATATTTTATTAAATTTTAATAATT
1 TTTATA-AAATTTAAAATTTTTATAT-TTTTATAAAAAATTAATAATT
* *
1668282 TTTATAAAATTTAATATTTTTAT-TATTTATAA
1 TTTATAAAATTTAAAATTTTTATATTTTTATAA
1668314 TTTTTTTCTA
Statistics
Matches: 65, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
44 2 0.03
45 17 0.26
46 33 0.51
47 6 0.09
48 7 0.11
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (46 bp):
TTTATAAAATTTAAAATTTTTATATTTTTATAAAAAATTAATAATT
Found at i:1668274 original size:18 final size:18
Alignment explanation
Indices: 1668253--1668306 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
1668243 AATTTAAAAT
1668253 TTTTAATATTTTATTAAA
1 TTTTAATATTTTATTAAA
1668271 TTTTAATAATTTT-TATAAA
1 TTTTAAT-ATTTTAT-TAAA
*
1668290 ATTTAATATTTTTATTA
1 TTTTAATA-TTTTATTA
1668307 TTTATAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 9 0.29
19 21 0.68
20 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTAATATTTTATTAAA
Found at i:1668458 original size:89 final size:90
Alignment explanation
Indices: 1668339--1668536 Score: 239
Period size: 89 Copynumber: 2.2 Consensus size: 90
1668329 TAATAAGAGT
*
1668339 AGGGGCTTAA-T--TTTTTTTTGAAAAATTTTGAGGGTCTTTTTGATAT-ATTTTGAAAGTTCAA
1 AGGGGCTTAATTACTTTTTTTTGAAAAATTTTGAGAG-CTTTTT-ATATCATTTTGAAAGTTCAA
* ** *
1668400 GTACCCAATTGAGTG-GGAAAAAAAGT
64 GTACACAATTGAGTGAAAAAAAAAAGG
*
1668426 A-GGGCTTAATTACTTTTTTTTGAAGAAA-TTTGAGAGCTTTTTTTATGCATTTTGAAAGTTCAA
1 AGGGGCTTAATTACTTTTTTTTGAA-AAATTTTGAGAGCTTTTTATAT-CATTTTGAAAGTTCAA
*
1668489 GTGCACAATTGAGTGAAAAAAAAAAGG
64 GTACACAATTGAGTGAAAAAAAAAAGG
*
1668516 AGGGGCTTAATTGCTTTTTTT
1 AGGGGCTTAATTACTTTTTTT
1668537 GAATAAGTTT
Statistics
Matches: 95, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
86 8 0.08
87 5 0.05
88 6 0.06
89 46 0.48
90 12 0.13
91 18 0.19
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.39
Consensus pattern (90 bp):
AGGGGCTTAATTACTTTTTTTTGAAAAATTTTGAGAGCTTTTTATATCATTTTGAAAGTTCAAGT
ACACAATTGAGTGAAAAAAAAAAGG
Found at i:1668557 original size:89 final size:87
Alignment explanation
Indices: 1668339--1668561 Score: 220
Period size: 89 Copynumber: 2.5 Consensus size: 87
1668329 TAATAAGAGT
* * * *
1668339 AGGGGCTTAATT-TTTTTTTGAAAAATTTTGAGGGTCTTTTTGATATATTTTGAAAGTTCAAGTA
1 AGGGGCTTAATTCTTTTTTTGAAAAAATTT-AAGGACTTTTTGATACATTTTGAAAGTTCAAGTA
* ** *
1668403 CCCAATTGAGTGGGAAAAAAAGT
65 CACAATTGAGTGAAAAAAAAAGG
* * * *
1668426 A-GGGCTTAATTACTTTTTTTTGAAGAAATTTGA-GAGCTTTTTTTATGCATTTTGAAAGTTCAA
1 AGGGGCTTAATT-C-TTTTTTTGAAAAAATTTAAGGA-C-TTTTTGATACATTTTGAAAGTTCAA
*
1668489 GTGCACAATTGAGTGAAAAAAAAAAGG
62 GTACACAATTGAGTG-AAAAAAAAAGG
* *
1668516 AGGGGCTTAATTGCTTTTTTTGAATAAGTTTAAGGACTTTTT-ATAC
1 AGGGGCTTAATT-CTTTTTTTGAAAAAATTTAAGGACTTTTTGATAC
1668562 CCTTAAGCCA
Statistics
Matches: 110, Mismatches: 18, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
86 10 0.09
87 2 0.02
88 4 0.04
89 55 0.50
90 26 0.24
91 13 0.12
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.39
Consensus pattern (87 bp):
AGGGGCTTAATTCTTTTTTTGAAAAAATTTAAGGACTTTTTGATACATTTTGAAAGTTCAAGTAC
ACAATTGAGTGAAAAAAAAAGG
Found at i:1672907 original size:30 final size:30
Alignment explanation
Indices: 1672846--1672918 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
1672836 TATCGACACC
*
1672846 ACACGGCCGTGTGGTAGGCCATGTACAATG
1 ACACGACCGTGTGGTAGGCCATGTACAATG
* * *
1672876 ACATGACCGTGTGGTAGGCCGTG-AGCGATG
1 ACACGACCGTGTGGTAGGCCATGTA-CAATG
*
1672906 ACACGGCCGTGTG
1 ACACGACCGTGTG
1672919 CAAGACAAGG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 1 0.03
30 35 0.97
ACGTcount: A:0.21, C:0.23, G:0.37, T:0.19
Consensus pattern (30 bp):
ACACGACCGTGTGGTAGGCCATGTACAATG
Found at i:1686122 original size:46 final size:46
Alignment explanation
Indices: 1686069--1686886 Score: 1636
Period size: 46 Copynumber: 17.8 Consensus size: 46
1686059 TACTTGAGTT
1686069 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1686115 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1686161 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1686207 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1686253 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1686299 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1686345 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1686391 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1686437 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1686483 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1686529 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1686575 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1686621 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1686667 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1686713 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1686759 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1686805 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1686851 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1686887 GCGGGTTACA
Statistics
Matches: 772, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 772 1.00
ACGTcount: A:0.19, C:0.24, G:0.30, T:0.26
Consensus pattern (46 bp):
CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:1688265 original size:11 final size:10
Alignment explanation
Indices: 1688226--1688301 Score: 53
Period size: 11 Copynumber: 7.1 Consensus size: 10
1688216 TGAGGGCGTT
1688226 ACAAAGACAGC
1 ACAAA-ACAGC
*
1688237 ACCAAAGCAGC
1 A-CAAAACAGC
1688248 ATCAAAACAGC
1 A-CAAAACAGC
*
1688259 ATCAAAATAGC
1 A-CAAAACAGC
* *
1688270 ACCAAACGGC
1 ACAAAACAGC
* *
1688280 AAAAAAATAGC
1 -ACAAAACAGC
1688291 ACAAAACAGC
1 ACAAAACAGC
1688301 A
1 A
1688302 GCAGTGAAAA
Statistics
Matches: 50, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
10 15 0.30
11 31 0.62
12 4 0.08
ACGTcount: A:0.55, C:0.26, G:0.13, T:0.05
Consensus pattern (10 bp):
ACAAAACAGC
Found at i:1688270 original size:22 final size:21
Alignment explanation
Indices: 1688226--1688301 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
1688216 TGAGGGCGTT
* **
1688226 ACAAAGACAGCACCAAAGCAGC
1 ACAAA-ACAGCAACAAAATAGC
*
1688248 ATCAAAACAGCATCAAAATAGC
1 A-CAAAACAGCAACAAAATAGC
* * *
1688270 ACCAAACGGCAAAAAAATAGC
1 ACAAAACAGCAACAAAATAGC
1688291 ACAAAACAGCA
1 ACAAAACAGCA
1688302 GCAGTGAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
21 25 0.57
22 15 0.34
23 4 0.09
ACGTcount: A:0.55, C:0.26, G:0.13, T:0.05
Consensus pattern (21 bp):
ACAAAACAGCAACAAAATAGC
Found at i:1688506 original size:9 final size:9
Alignment explanation
Indices: 1688489--1688524 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
1688479 ATCGAAGAAA
*
1688489 CATCATCCT
1 CATCGTCCT
1688498 CATCGTCCT
1 CATCGTCCT
*
1688507 CATCGTCAT
1 CATCGTCCT
1688516 CATCGTCCT
1 CATCGTCCT
1688525 TGCAACCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.17, C:0.42, G:0.08, T:0.33
Consensus pattern (9 bp):
CATCGTCCT
Found at i:1699249 original size:19 final size:18
Alignment explanation
Indices: 1699221--1699259 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1699211 AAGTTTATAT
1699221 TTCCTACTGATTTTGTAA
1 TTCCTACTGATTTTGTAA
*
1699239 TNTCCTGCTGATTTTGTAA
1 T-TCCTACTGATTTTGTAA
1699258 TT
1 TT
1699260 TTAGATTTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.18, C:0.15, G:0.13, T:0.51
Consensus pattern (18 bp):
TTCCTACTGATTTTGTAA
Found at i:1709433 original size:26 final size:27
Alignment explanation
Indices: 1709382--1709434 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
1709372 TTGCCTTAAA
*
1709382 TTCAAATCTTTTTGAGTCATTAAATAT
1 TTCAAATCTTTTTGAGTCAGTAAATAT
*
1709409 TTCAAA-CTTTTGTGA-TCAGTGAATAT
1 TTCAAATCTTTT-TGAGTCAGTAAATAT
1709435 GTGGCACTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.45
Consensus pattern (27 bp):
TTCAAATCTTTTTGAGTCAGTAAATAT
Found at i:1713004 original size:48 final size:48
Alignment explanation
Indices: 1712949--1713043 Score: 181
Period size: 48 Copynumber: 2.0 Consensus size: 48
1712939 ATCAAATTTC
*
1712949 TTATTCTTTGAACATAAGTATATCAAATTCATAATTTCGAGGAAACTA
1 TTATTCTTTGAACATAAGTATATCAAATTCATAATTTCGAGAAAACTA
1712997 TTATTCTTTGAACATAAGTATATCAAATTCATAATTTCGAGAAAACT
1 TTATTCTTTGAACATAAGTATATCAAATTCATAATTTCGAGAAAACT
1713044 GTTGTTCTGA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (48 bp):
TTATTCTTTGAACATAAGTATATCAAATTCATAATTTCGAGAAAACTA
Found at i:1714858 original size:53 final size:54
Alignment explanation
Indices: 1714768--1714983 Score: 242
Period size: 55 Copynumber: 4.0 Consensus size: 54
1714758 TACGTGGTAT
* * *
1714768 CCTTTTGAAACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTG
1 CCTTATGAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTG
* *
1714822 CCTTATG-AACTCACCAATGCCATGCCTTGGCATGGTCTTACATGAG-A-CCTTTG
1 CCTTATGAAACTTACCAATGCCATGCCTTGACATGGTCTTACATG-GTATCC-TTG
* * * * * *
1714875 CCTTATAGTAACTTATCAATGCCATGTCTTGACATGGACTTACATGATTTCCTTG
1 CCTTAT-GAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTG
* *
1714930 CCTTA-GAAACCTTACCAATTTCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 CCTTATGAAA-CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTATCCTT
1714984 AAACCCTAAT
Statistics
Matches: 134, Mismatches: 20, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
52 2 0.01
53 46 0.34
54 15 0.11
55 69 0.51
56 2 0.01
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (54 bp):
CCTTATGAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTG
Found at i:1719026 original size:61 final size:60
Alignment explanation
Indices: 1718900--1719026 Score: 161
Period size: 61 Copynumber: 2.1 Consensus size: 60
1718890 TTTTAGTAAG
* * ** *
1718900 ATTATTGTTAAATATATTTTCGTAGAAATAATATTAAATAATTTAATCATATTTTAACATA
1 ATTATTATTAAATAAATTTTAATAGAAATAATATT-AATAATTTAATAATATTTTAACATA
*
1718961 ATTATTATTAAATAAATTTTAATA-AAATAATA-T-ATAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATAAATTTTAATAGAAATAATATTAATAATTTAATAATA-TTTTAACATA
1719019 ATTATTAT
1 ATTATTAT
1719027 AATATGAATT
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
57 13 0.22
58 17 0.29
59 1 0.02
60 8 0.14
61 20 0.34
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (60 bp):
ATTATTATTAAATAAATTTTAATAGAAATAATATTAATAATTTAATAATATTTTAACATA
Found at i:1719049 original size:58 final size:57
Alignment explanation
Indices: 1718937--1719056 Score: 145
Period size: 58 Copynumber: 2.1 Consensus size: 57
1718927 ATAATATTAA
* **
1718937 ATAATTTAATCATATTTTAACATAATTATTATTAAATAAATTTTAATAAAATAATAT
1 ATAATTTAATAATATTTTAACATAATTATTATTAAATAAATTACAATAAAATAATAT
* * *
1718994 ATAATTTAATAATATTTTTAATATAATTATTA-TAATATGAATTACAA-AATCATAATAT
1 ATAATTTAATAATA-TTTTAACATAATTATTATTAA-ATAAATTACAATAA-AATAATAT
1719052 ATAAT
1 ATAAT
1719057 ATTATAAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
57 18 0.33
58 36 0.67
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (57 bp):
ATAATTTAATAATATTTTAACATAATTATTATTAAATAAATTACAATAAAATAATAT
Found at i:1719065 original size:23 final size:21
Alignment explanation
Indices: 1719034--1719076 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1719024 TATAATATGA
1719034 ATTACAAAATCATAATATATAAT
1 ATTACAAAA--ATAATATATAAT
*
1719057 ATTATAAAAATAATATATAA
1 ATTACAAAAATAATATATAA
1719077 CCTACGTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
ATTACAAAAATAATATATAAT
Found at i:1722424 original size:17 final size:17
Alignment explanation
Indices: 1722383--1722425 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1722373 ACGCTCAACA
*
1722383 AAACAATTTACGAAAAC
1 AAACATTTTACGAAAAC
** *
1722400 AATGATTTTACGTAAAC
1 AAACATTTTACGAAAAC
1722417 AAACATTTT
1 AAACATTTT
1722426 TGAGAACACA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.30
Consensus pattern (17 bp):
AAACATTTTACGAAAAC
Found at i:1732034 original size:127 final size:127
Alignment explanation
Indices: 1731893--1732147 Score: 501
Period size: 127 Copynumber: 2.0 Consensus size: 127
1731883 TTTCACTTGA
*
1731893 ACTAAAAAATTATTTAAATAAGGTCTTATTTTCTTTTATTTTGTATTAACTCAATTCGTTTATAG
1 ACTAAAAAAATATTTAAATAAGGTCTTATTTTCTTTTATTTTGTATTAACTCAATTCGTTTATAG
1731958 GTATACAATGTGTTAAATATCTTAAAAATTATGTATTTTAAAATATTCGATTATTATTATTT
66 GTATACAATGTGTTAAATATCTTAAAAATTATGTATTTTAAAATATTCGATTATTATTATTT
1732020 ACTAAAAAAATATTTAAATAAGGTCTTATTTTCTTTTATTTTGTATTAACTCAATTCGTTTATAG
1 ACTAAAAAAATATTTAAATAAGGTCTTATTTTCTTTTATTTTGTATTAACTCAATTCGTTTATAG
1732085 GTATACAATGTGTTAAATATCTTAAAAATTATGTATTTTAAAATATTCGATTATTATTATTT
66 GTATACAATGTGTTAAATATCTTAAAAATTATGTATTTTAAAATATTCGATTATTATTATTT
1732147 A
1 A
1732148 AATAAAATAT
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
127 127 1.00
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.48
Consensus pattern (127 bp):
ACTAAAAAAATATTTAAATAAGGTCTTATTTTCTTTTATTTTGTATTAACTCAATTCGTTTATAG
GTATACAATGTGTTAAATATCTTAAAAATTATGTATTTTAAAATATTCGATTATTATTATTT
Found at i:1732554 original size:29 final size:27
Alignment explanation
Indices: 1732498--1732557 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 27
1732488 TAACATAAAG
*
1732498 TAAAAATATCAAAAATAAAAATAGTTT
1 TAAAAATATCAAAAATAAAAATAATTT
* *
1732525 TAAAATATATTAAAAGATTAAAATAATTT
1 TAAAA-ATATCAAAA-ATAAAAATAATTT
1732554 TAAA
1 TAAA
1732558 CGAAATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 5 0.18
28 8 0.29
29 15 0.54
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (27 bp):
TAAAAATATCAAAAATAAAAATAATTT
Found at i:1745290 original size:20 final size:20
Alignment explanation
Indices: 1745245--1745291 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
1745235 TTTTTAATCC
* *
1745245 ATTAAATAATATATTTTATA
1 ATTAAAAAACATATTTTATA
1745265 ATTTAAAAAACATA-TTTACTA
1 A-TTAAAAAACATATTTTA-TA
1745286 ATTAAA
1 ATTAAA
1745292 TTAGAATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (20 bp):
ATTAAAAAACATATTTTATA
Found at i:1745843 original size:18 final size:21
Alignment explanation
Indices: 1745820--1745865 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1745810 ACTATTTCTC
1745820 TAATAATAA-AA-AT-ATTAT
1 TAATAATAACAATATAATTAT
1745838 TAATAA-AACAATTATAATTAT
1 TAATAATAACAA-TATAATTAT
1745859 TAATAAT
1 TAATAAT
1745866 TTGTTATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 2 0.09
18 8 0.35
20 2 0.09
21 11 0.48
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
TAATAATAACAATATAATTAT
Found at i:1746461 original size:19 final size:19
Alignment explanation
Indices: 1746437--1746473 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1746427 AATATAAATT
*
1746437 ATTTATAAATTTTATTTAA
1 ATTTATAAATTATATTTAA
1746456 ATTTATAAATTATATTTA
1 ATTTATAAATTATATTTA
1746474 TGATTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTATAAATTATATTTAA
Found at i:1753704 original size:24 final size:26
Alignment explanation
Indices: 1753677--1753736 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 26
1753667 TTCATGTTTT
*
1753677 CATGGTAAAAATT-A-ACATATAATA
1 CATGGTAAAAATTAAGACACATAATA
*
1753701 CAT-G-AAACATTAAGACACATAATA
1 CATGGTAAAAATTAAGACACATAATA
*
1753725 CATGGTAGAAAT
1 CATGGTAAAAAT
1753737 GAAATATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
22 6 0.21
23 2 0.07
24 15 0.54
25 1 0.04
26 4 0.14
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.25
Consensus pattern (26 bp):
CATGGTAAAAATTAAGACACATAATA
Found at i:1766385 original size:10 final size:10
Alignment explanation
Indices: 1766370--1766395 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1766360 CTAAATTTGG
1766370 AAAATTGTAA
1 AAAATTGTAA
1766380 AAAATTGTAA
1 AAAATTGTAA
1766390 AAAATT
1 AAAATT
1766396 AATTAGGGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (10 bp):
AAAATTGTAA
Found at i:1767230 original size:23 final size:24
Alignment explanation
Indices: 1767204--1767248 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1767194 ATATCCCCAC
*
1767204 ATGGAGTGTAGGGT-TGGATGGAA
1 ATGGAGTGTAGAGTCTGGATGGAA
*
1767227 ATGGTGTGTAGAGTCTGGATGG
1 ATGGAGTGTAGAGTCTGGATGG
1767249 GTAAGATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.22, C:0.02, G:0.47, T:0.29
Consensus pattern (24 bp):
ATGGAGTGTAGAGTCTGGATGGAA
Found at i:1770668 original size:25 final size:25
Alignment explanation
Indices: 1770634--1770703 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 25
1770624 CAGGCCCATT
*
1770634 TCACAACTCGTGTGAGCATTTACAA
1 TCACAACTCGTCTGAGCATTTACAA
* **
1770659 TCACAGCTCGTCTGAGCATTTACCG
1 TCACAACTCGTCTGAGCATTTACAA
* *
1770684 TCACAACTTGTTTGAGCATT
1 TCACAACTCGTCTGAGCATT
1770704 GTTCCTACAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (25 bp):
TCACAACTCGTCTGAGCATTTACAA
Found at i:1770825 original size:13 final size:13
Alignment explanation
Indices: 1770762--1770828 Score: 57
Period size: 13 Copynumber: 5.2 Consensus size: 13
1770752 TGAGTAAACA
*
1770762 GAAATGGTAATAT
1 GAAATGGTTATAT
*
1770775 G-AATGGATATACT
1 GAAATGGTTATA-T
*
1770788 -AAATGTTTATAT
1 GAAATGGTTATAT
* *
1770800 GAAAATAGATATAT
1 G-AAATGGTTATAT
1770814 GAAATGGTTATAT
1 GAAATGGTTATAT
1770827 GA
1 GA
1770829 GTTGTTTATG
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
12 9 0.22
13 22 0.54
14 10 0.24
ACGTcount: A:0.45, C:0.01, G:0.19, T:0.34
Consensus pattern (13 bp):
GAAATGGTTATAT
Found at i:1778714 original size:15 final size:16
Alignment explanation
Indices: 1778694--1778728 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1778684 TTGGAGAATG
*
1778694 AAAAGAAAGGAAAG-A
1 AAAAGAAAGAAAAGTA
1778709 AAAAGAAAGAAAAGTA
1 AAAAGAAAGAAAAGTA
1778725 AAAA
1 AAAA
1778729 TGATTGATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (16 bp):
AAAAGAAAGAAAAGTA
Found at i:1794863 original size:17 final size:18
Alignment explanation
Indices: 1794828--1794866 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1794818 AACCTGTTCA
1794828 GGCCGTGTGATCATACAC
1 GGCCGTGTGATCATACAC
*
1794846 GGCCGTGTGCTC-TACAC
1 GGCCGTGTGATCATACAC
1794863 GGCC
1 GGCC
1794867 ATGTAGTGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.15, C:0.33, G:0.31, T:0.21
Consensus pattern (18 bp):
GGCCGTGTGATCATACAC
Found at i:1800675 original size:13 final size:13
Alignment explanation
Indices: 1800654--1800693 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
1800644 TAAGTAATCG
1800654 CACACGGGCGTGT
1 CACACGGGCGTGT
*
1800667 CACATGGGCGTGT
1 CACACGGGCGTGT
*
1800680 TACACGGGCGTGT
1 CACACGGGCGTGT
1800693 C
1 C
1800694 CCTACCGAGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.15, C:0.28, G:0.38, T:0.20
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:1804481 original size:51 final size:51
Alignment explanation
Indices: 1804405--1804507 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
1804395 TTCGGTACGG
1804405 TGGAGGTGAGTCATCCTAAGTTCGGCACTTTTAAGGTAAACAACACCCGTT
1 TGGAGGTGAGTCATCCTAAGTTCGGCACTTTTAAGGTAAACAACACCCGTT
1804456 TGGAGGTGAGTCATCCTAAGTTCGGCACTTTTAAGGTAAACAACACCCGTT
1 TGGAGGTGAGTCATCCTAAGTTCGGCACTTTTAAGGTAAACAACACCCGTT
1804507 T
1 T
1804508 AAAACCTTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.28
Consensus pattern (51 bp):
TGGAGGTGAGTCATCCTAAGTTCGGCACTTTTAAGGTAAACAACACCCGTT
Found at i:1819771 original size:13 final size:13
Alignment explanation
Indices: 1819755--1819787 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1819745 TTTAATTAAA
*
1819755 TTAGTTAATTAGT
1 TTAGATAATTAGT
1819768 TTAGATAATTAGT
1 TTAGATAATTAGT
1819781 TTA-ATAA
1 TTAGATAA
1819788 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Done.