Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008478.1 Hibiscus syriacus cultivar Beakdansim tig00111309_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: 1476524
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1307958 original size:21 final size:21
Alignment explanation
Indices: 1307929--1308073 Score: 113
Period size: 21 Copynumber: 6.8 Consensus size: 21
1307919 ATTTTTGTGC
1307929 ATAGAGTATCGATACCCCTTAG
1 ATAG-GTATCGATACCCCTTAG
*
1307951 ACT-GGTATCGATACCCCCTTTG
1 A-TAGGTATCGATA-CCCCTTAG
1307973 AATAGGTATCGATACCCCTTCA-
1 -ATAGGTATCGATACCCCTT-AG
1307995 ATAGGTATCGATACCCCTTCA-
1 ATAGGTATCGATACCCCTT-AG
*
1308016 ATAAGTATCGATACCATCCTT-G
1 ATAGGTATCGATACC--CCTTAG
* * *
1308038 AATGGGTATCAATACCCCCT-G
1 -ATAGGTATCGATACCCCTTAG
*
1308059 AT-GGTACCGATACCC
1 ATAGGTATCGATACCC
1308074 TCCACGGGGT
Statistics
Matches: 105, Mismatches: 9, Indels: 21
0.78 0.07 0.16
Matches are distributed among these distances:
19 11 0.10
20 2 0.02
21 48 0.46
22 16 0.15
23 28 0.27
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (21 bp):
ATAGGTATCGATACCCCTTAG
Found at i:1308002 original size:44 final size:42
Alignment explanation
Indices: 1307929--1308057 Score: 136
Period size: 44 Copynumber: 2.9 Consensus size: 42
1307919 ATTTTTGTGC
*
1307929 ATAGAGTATCGATACCCCTTAGACTGGTATCGATACCCCCTTTGA
1 ATAG-GTATCGATACCCCTTA-A-TGGTATCGATACCCCCTTTCA
1307974 ATAGGTATCGATACCCCTTCAATAGGTATCGATA-CCCC-TTCA
1 ATAGGTATCGATACCCCTT-AAT-GGTATCGATACCCCCTTTCA
* *
1308016 ATAAGTATCGATACCATCCTTGAATGGGTATCAATACCCCCT
1 ATAGGTATCGATACC--CCTT-AAT-GGTATCGATACCCCCT
1308058 GATGGTACCG
Statistics
Matches: 73, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
42 17 0.23
43 5 0.07
44 42 0.58
45 9 0.12
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (42 bp):
ATAGGTATCGATACCCCTTAATGGTATCGATACCCCCTTTCA
Found at i:1308039 original size:65 final size:66
Alignment explanation
Indices: 1307929--1308055 Score: 163
Period size: 65 Copynumber: 1.9 Consensus size: 66
1307919 ATTTTTGTGC
* *
1307929 ATAGAGTATCGATACCCCTTAGACTGGTATCGATACCCCCTTTGAATAGGTATCGATACCCCTTC
1 ATAGAGTATCGATACCCCTTAGACTAGTATCGATACCCCCTTTGAATAGGTATCAATACCCCTTC
1307994 A
66 A
* *
1307995 ATAG-GTATCGATACCCCTTCA-A-TAAGTATCGATACCATCC-TTGAATGGGTATCAATACCCC
1 ATAGAGTATCGATACCCCTT-AGACT-AGTATCGATACC-CCCTTTGAATAGGTATCAATACCCC
1308056 CTGATGGTAC
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
64 1 0.02
65 46 0.85
66 7 0.13
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (66 bp):
ATAGAGTATCGATACCCCTTAGACTAGTATCGATACCCCCTTTGAATAGGTATCAATACCCCTTC
A
Found at i:1310843 original size:20 final size:19
Alignment explanation
Indices: 1310778--1310852 Score: 80
Period size: 18 Copynumber: 3.8 Consensus size: 19
1310768 GAATGCTCGA
*
1310778 ATGGTACCGATACCCCCAT
1 ATGGTACCGATACCCCCAG
*
1310797 A-GGTATCGATACCCCCATG
1 ATGGTACCGATACCCCCA-G
*
1310816 CAATGGTATCGATACCCCTCAG
1 --ATGGTACCGATACCCC-CAG
1310838 ATGGTACCGATACCC
1 ATGGTACCGATACCC
1310853 TAAGGCATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
18 15 0.31
19 1 0.02
20 14 0.29
21 1 0.02
22 15 0.31
23 2 0.04
ACGTcount: A:0.27, C:0.33, G:0.19, T:0.21
Consensus pattern (19 bp):
ATGGTACCGATACCCCCAG
Found at i:1311516 original size:29 final size:29
Alignment explanation
Indices: 1311474--1311533 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
1311464 ACAAAAGCTT
1311474 CCACCAAATTTTTAATTGCCAATTCACCC
1 CCACCAAATTTTTAATTGCCAATTCACCC
1311503 CCACCAAATTTTTAATTGCCAATTCACCC
1 CCACCAAATTTTTAATTGCCAATTCACCC
1311532 CC
1 CC
1311534 CTCTTGGCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.30, C:0.37, G:0.03, T:0.30
Consensus pattern (29 bp):
CCACCAAATTTTTAATTGCCAATTCACCC
Found at i:1314328 original size:15 final size:15
Alignment explanation
Indices: 1314308--1314353 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
1314298 TGCTTTCAAC
1314308 TTTTCTTTCTT-TTCT
1 TTTTCTTT-TTCTTCT
1314323 TTTTCTTTTTCTTC-
1 TTTTCTTTTTCTTCT
*
1314337 TTTT-GTTTTCTTCT
1 TTTTCTTTTTCTTCT
1314351 TTT
1 TTT
1314354 GAGTGCTTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 8 0.29
14 9 0.32
15 11 0.39
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (15 bp):
TTTTCTTTTTCTTCT
Found at i:1314347 original size:13 final size:13
Alignment explanation
Indices: 1314317--1314354 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
1314307 CTTTTCTTTC
1314317 TTTTCTT-TTTCT-
1 TTTTCTTCTTT-TG
1314329 TTTTCTTCTTTTG
1 TTTTCTTCTTTTG
1314342 TTTTCTTCTTTTG
1 TTTTCTTCTTTTG
1314355 AGTGCTTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (13 bp):
TTTTCTTCTTTTG
Found at i:1316454 original size:23 final size:24
Alignment explanation
Indices: 1316423--1316467 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
1316413 CATCAATTTA
1316423 TCAAGCCTTGTGGAGAAGCATGTG
1 TCAAGCCTTGTGGAGAAGCATGTG
1316447 TCAA-CCTTGTGGAGAAGCATG
1 TCAAGCCTTGTGGAGAAGCATG
1316468 CAACTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (24 bp):
TCAAGCCTTGTGGAGAAGCATGTG
Found at i:1316547 original size:17 final size:17
Alignment explanation
Indices: 1316525--1316563 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
1316515 TGTTATTAAC
*
1316525 ATTATTAAATCATCATT
1 ATTATTAAATAATCATT
1316542 ATTATTAAATAATCATT
1 ATTATTAAATAATCATT
1316559 ATTAT
1 ATTAT
1316564 ACCATTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTATTAAATAATCATT
Found at i:1322379 original size:102 final size:103
Alignment explanation
Indices: 1322202--1322404 Score: 399
Period size: 102 Copynumber: 2.0 Consensus size: 103
1322192 TTAACAGAAA
1322202 TACCTTAAAATAAAAGAAATATTTCAAAACTACCTTTTCATTTATGATAAATCCCTAGTTTTATT
1 TACCTTAAAATAAAAGAAATATTTCAAAACTACCTTTTCATTTATGATAAATCCCTAGTTTTATT
1322267 TTGTCCGTTGATTAGAAAAAAAATTCAATTTCTTCTGG
66 TTGTCCGTTGATTAGAAAAAAAATTCAATTTCTTCTGG
1322305 TACCTTAAAAT-AAAGAAATATTTCAAAACTACCTTTTCATTTATGATAAATCCCTAGTTTTATT
1 TACCTTAAAATAAAAGAAATATTTCAAAACTACCTTTTCATTTATGATAAATCCCTAGTTTTATT
1322369 TTGTCCGTTGATTAGAAAAAAAATTCAATTTCTTCT
66 TTGTCCGTTGATTAGAAAAAAAATTCAATTTCTTCT
1322405 CTGGTTTTCT
Statistics
Matches: 100, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
102 89 0.89
103 11 0.11
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (103 bp):
TACCTTAAAATAAAAGAAATATTTCAAAACTACCTTTTCATTTATGATAAATCCCTAGTTTTATT
TTGTCCGTTGATTAGAAAAAAAATTCAATTTCTTCTGG
Found at i:1326258 original size:22 final size:20
Alignment explanation
Indices: 1326231--1326271 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
1326221 TAATGTATAC
*
1326231 ATTTTATTAAAATATATAAATA
1 ATTTTATCAAAA-AT-TAAATA
1326253 ATTTTATCAAAAATTAAAT
1 ATTTTATCAAAAATTAAAT
1326272 GTAATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 2 0.11
22 11 0.61
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTTTATCAAAAATTAAATA
Found at i:1329477 original size:35 final size:36
Alignment explanation
Indices: 1329435--1329505 Score: 117
Period size: 35 Copynumber: 2.0 Consensus size: 36
1329425 TGGCAACCAA
*
1329435 CTTTGAAAAATGTTTTTC-AAGTTTGGTAAATGTTT
1 CTTTGAAAAATATTTTTCAAAGTTTGGTAAATGTTT
*
1329470 CTTTGAAAAATATTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATATTTTTCAAAGTTTGGTAAATGTTT
1329506 GTTGGAAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
35 17 0.52
36 16 0.48
ACGTcount: A:0.30, C:0.06, G:0.17, T:0.48
Consensus pattern (36 bp):
CTTTGAAAAATATTTTTCAAAGTTTGGTAAATGTTT
Found at i:1329937 original size:16 final size:17
Alignment explanation
Indices: 1329916--1329947 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1329906 TACTATTCAT
1329916 GTGAATAGT-AAATTTC
1 GTGAATAGTGAAATTTC
1329932 GTGAATAGTGAAATTT
1 GTGAATAGTGAAATTT
1329948 TGTCGGCGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.38
Consensus pattern (17 bp):
GTGAATAGTGAAATTTC
Found at i:1334284 original size:32 final size:33
Alignment explanation
Indices: 1334238--1334313 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 33
1334228 GGCAACCAAC
1334238 TTTGAAAAATGTTTTTC-AAGTTTGGTAAATGTT
1 TTTG-AAAATGTTTTTCAAAGTTTGGTAAATGTT
*
1334271 TTTGAAAATGTTTTTCAAAGTTTGGTAGATGTT
1 TTTGAAAATGTTTTTCAAAGTTTGGTAAATGTT
1334304 TGTTGAAAAT
1 T-TTGAAAAT
1334314 AGGAATGGGT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
32 12 0.30
33 20 0.50
34 8 0.20
ACGTcount: A:0.30, C:0.03, G:0.20, T:0.47
Consensus pattern (33 bp):
TTTGAAAATGTTTTTCAAAGTTTGGTAAATGTT
Found at i:1335958 original size:3 final size:3
Alignment explanation
Indices: 1335952--1336005 Score: 90
Period size: 3 Copynumber: 17.3 Consensus size: 3
1335942 AATGATGATG
1335952 ATT ATT ATT ATT ATAT ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT
1 ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT
1335999 ATT ATT A
1 ATT ATT A
1336006 GGGTAAAGTA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
3 43 0.88
4 6 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1335986 original size:25 final size:25
Alignment explanation
Indices: 1335953--1336005 Score: 90
Period size: 25 Copynumber: 2.1 Consensus size: 25
1335943 ATGATGATGA
1335953 TTATTATTATTA-TATATTATTATTA
1 TTATTATTATTATTAT-TTATTATTA
1335978 TTATTATTATTATTATTTATTATTA
1 TTATTATTATTATTATTTATTATTA
1336003 TTA
1 TTA
1336006 GGGTAAAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 24 0.89
26 3 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (25 bp):
TTATTATTATTATTATTTATTATTA
Found at i:1336122 original size:30 final size:31
Alignment explanation
Indices: 1336083--1336149 Score: 109
Period size: 30 Copynumber: 2.2 Consensus size: 31
1336073 CTTGTATACA
* *
1336083 GTCCTCCAACATTTAGTCTA-TTGCAATATG
1 GTCCCCCAACATTTAGTCCATTTGCAATATG
1336113 GTCCCCCAACATTTAGTCCATTTGCAATATG
1 GTCCCCCAACATTTAGTCCATTTGCAATATG
1336144 GTCCCC
1 GTCCCC
1336150 ACCGTAACTG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 18 0.53
31 16 0.47
ACGTcount: A:0.24, C:0.30, G:0.13, T:0.33
Consensus pattern (31 bp):
GTCCCCCAACATTTAGTCCATTTGCAATATG
Found at i:1340816 original size:36 final size:37
Alignment explanation
Indices: 1340732--1340828 Score: 117
Period size: 39 Copynumber: 2.6 Consensus size: 37
1340722 AAAATGGTGC
*
1340732 TCTAGGCGTCTTTAACACAATTGCATTCAAACATGGAGG
1 TCTAGGCGTCTTTAACACAATTACATTCAAACAT-G-GG
*
1340771 TCTAGGCGTCTTTAACACAACTTACA-TCGAACAT-GG
1 TCTAGGCGTCTTTAACACAA-TTACATTCAAACATGGG
* *
1340807 TCTCGGCGTCTTTAACATAATT
1 TCTAGGCGTCTTTAACACAATT
1340829 CATGGAGGTC
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
35 2 0.04
36 20 0.38
39 27 0.51
40 4 0.08
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (37 bp):
TCTAGGCGTCTTTAACACAATTACATTCAAACATGGG
Found at i:1340970 original size:19 final size:20
Alignment explanation
Indices: 1340946--1340985 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1340936 GCTGGACGTG
1340946 GGAAA-TCACGGGGTGAGCA
1 GGAAATTCACGGGGTGAGCA
*
1340965 GGAAATTCATGGGGTGAGCA
1 GGAAATTCACGGGGTGAGCA
1340985 G
1 G
1340986 AGAATATGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.30, C:0.12, G:0.42, T:0.15
Consensus pattern (20 bp):
GGAAATTCACGGGGTGAGCA
Found at i:1341085 original size:30 final size:29
Alignment explanation
Indices: 1341045--1341152 Score: 112
Period size: 30 Copynumber: 3.6 Consensus size: 29
1341035 AGTATAGGAT
* *
1341045 TTCTCGGCGTCTTCTTCACTTTGGGTGGA
1 TTCTCAGCGTCTTCTTCACTTGGGGTGGA
1341074 TTGCTCAGCGTCTTCTTCA-TTGGGGGTGGAA
1 TT-CTCAGCGTCTTCTTCACTT-GGGGTGG-A
* * *
1341105 TACTCGGCGT-TTCTTCACTTGGGAGGGGA
1 TTCTCAGCGTCTTCTTCACTTGGG-GTGGA
1341134 TATCTCAGCGTCTTCTTCA
1 T-TCTCAGCGTCTTCTTCA
1341153 GAATAATGCA
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
29 16 0.25
30 40 0.62
31 9 0.14
ACGTcount: A:0.12, C:0.23, G:0.28, T:0.37
Consensus pattern (29 bp):
TTCTCAGCGTCTTCTTCACTTGGGGTGGA
Found at i:1343891 original size:14 final size:14
Alignment explanation
Indices: 1343862--1344104 Score: 166
Period size: 14 Copynumber: 17.8 Consensus size: 14
1343852 GTAACTATTA
1343862 TTAAATCATT-AAG
1 TTAAATCATTAAAG
1343875 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* *
1343889 TT-AATTAATAATTA-
1 TTAAATCATTAA--AG
1343903 TTAAATCATTAAAG
1 TTAAATCATTAAAG
1343917 TT-AATCATTAAAG
1 TTAAATCATTAAAG
* * *
1343930 TTAAGTAATTATTA-
1 TTAAATCATTA-AAG
*
1343944 TTGAATCATTAAAG
1 TTAAATCATTAAAG
1343958 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* * *
1343972 TTAAGTAATT--AT
1 TTAAATCATTAAAG
*
1343984 TTGAATCATTAAA-
1 TTAAATCATTAAAG
*
1343997 TTAGATCATT-AAG
1 TTAAATCATTAAAG
* * *
1344010 TTAAGTAATTATTA-
1 TTAAATCATTA-AAG
*
1344024 TTGAATCATTAAAG
1 TTAAATCATTAAAG
*
1344038 TTAAATCATTGAAG
1 TTAAATCATTAAAG
* * *
1344052 TTAAGTAATTATTA-
1 TTAAATCATTA-AAG
*
1344066 TTAAATCATTAAAT
1 TTAAATCATTAAAG
*
1344080 TTAAATCATTAAAA
1 TTAAATCATTAAAG
*
1344094 TTAAATAATTA
1 TTAAATCATTA
1344105 TTATTAAATA
Statistics
Matches: 175, Mismatches: 39, Indels: 31
0.71 0.16 0.13
Matches are distributed among these distances:
12 10 0.06
13 49 0.28
14 105 0.60
15 11 0.06
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (14 bp):
TTAAATCATTAAAG
Found at i:1343978 original size:42 final size:42
Alignment explanation
Indices: 1343837--1344113 Score: 404
Period size: 42 Copynumber: 6.7 Consensus size: 42
1343827 TCATAAATAT
* *
1343837 AATCATTAAAGTCAAGTAACTATTATTAAATCATT-AAGTTA
1 AATCATTAAAGTTAAGTAATTATTATTAAATCATTAAAGTTA
* *
1343878 AATCATTAAAGTTAATTAATAATTATTAAATCATTAAAGTT-
1 AATCATTAAAGTTAAGTAATTATTATTAAATCATTAAAGTTA
*
1343919 AATCATTAAAGTTAAGTAATTATTATTGAATCATTAAAGTTA
1 AATCATTAAAGTTAAGTAATTATTATTAAATCATTAAAGTTA
*
1343961 AATCATTAAAGTTAAGTAATTA-T-TTGAATCATTAAA-TTA
1 AATCATTAAAGTTAAGTAATTATTATTAAATCATTAAAGTTA
* *
1344000 GATCATT-AAGTTAAGTAATTATTATTGAATCATTAAAGTTA
1 AATCATTAAAGTTAAGTAATTATTATTAAATCATTAAAGTTA
* *
1344041 AATCATTGAAGTTAAGTAATTATTATTAAATCATTAAATTTA
1 AATCATTAAAGTTAAGTAATTATTATTAAATCATTAAAGTTA
* *
1344083 AATCATTAAAATTAAATAATTATTATTAAAT
1 AATCATTAAAGTTAAGTAATTATTATTAAAT
1344114 ATGTACTCGA
Statistics
Matches: 216, Mismatches: 14, Indels: 11
0.90 0.06 0.05
Matches are distributed among these distances:
38 14 0.06
39 10 0.05
40 26 0.12
41 79 0.37
42 87 0.40
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (42 bp):
AATCATTAAAGTTAAGTAATTATTATTAAATCATTAAAGTTA
Found at i:1344005 original size:122 final size:122
Alignment explanation
Indices: 1343837--1344106 Score: 389
Period size: 122 Copynumber: 2.2 Consensus size: 122
1343827 TCATAAATAT
* * * *
1343837 AATCATTAAAGTCAAGTAACTATTATTAAATCATTAAGTTAAATCATTAAAGTTAATTAATAATT
1 AATCATTAAAGTTAAGTAATTA-T-TTAAATCATTAAATTAAATCATT-AAGTTAAGTAATAATT
*
1343902 ATTAAATCATTAAAGTT-AATCATTAAAGTTAAGTAATTATTATTGAATCATTAAAGTTA
63 ATTAAATCATTAAAGTTAAATCATTAAAGTTAAGTAATTATTATTAAATCATTAAAGTTA
* * *
1343961 AATCATTAAAGTTAAGTAATTATTTGAATCATTAAATTAGATCATTAAGTTAAGTAATTATTATT
1 AATCATTAAAGTTAAGTAATTATTTAAATCATTAAATTAAATCATTAAGTTAAGTAATAATTATT
* * *
1344026 GAATCATTAAAGTTAAATCATTGAAGTTAAGTAATTATTATTAAATCATTAAATTTA
66 AAATCATTAAAGTTAAATCATTAAAGTTAAGTAATTATTATTAAATCATTAAAGTTA
* *
1344083 AATCATTAAAATTAAATAATTATT
1 AATCATTAAAGTTAAGTAATTATT
1344107 ATTAAATATG
Statistics
Matches: 132, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
121 30 0.23
122 81 0.61
123 1 0.01
124 20 0.15
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (122 bp):
AATCATTAAAGTTAAGTAATTATTTAAATCATTAAATTAAATCATTAAGTTAAGTAATAATTATT
AAATCATTAAAGTTAAATCATTAAAGTTAAGTAATTATTATTAAATCATTAAAGTTA
Found at i:1347617 original size:81 final size:82
Alignment explanation
Indices: 1347466--1347659 Score: 257
Period size: 81 Copynumber: 2.4 Consensus size: 82
1347456 TATATTTTTT
* *
1347466 TTTTTGCTTTTGCTTTCTTTTATGCTATTTGGTGTGCTGTTTTCGATGGATAATTGCCCATTATC
1 TTTTT-CTTTTGCTTTATTTTATGCTATTTGGTGTGCTGTTTTAGAT-G-TAATTGCCCATTATC
1347531 ACATGCATTATTACCCTTTC
63 ACATGCATTATTACCCTTTC
* * * * * *
1347551 TTTTTCTTTTGGTTTATTTTATGTTGTTTTGTGTTCTGTTTTAGAT-TAATTGTCCATTATCACA
1 TTTTTCTTTTGCTTTATTTTATGCTATTTGGTGTGCTGTTTTAGATGTAATTGCCCATTATCACA
1347615 TGCATTATTACCCTTTC
66 TGCATTATTACCCTTTC
* *
1347632 TTTTACTTTT-CTTTATTTTGTGCTATTT
1 TTTTTCTTTTGCTTTATTTTATGCTATTT
1347660 TATAGGACCA
Statistics
Matches: 96, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
80 14 0.15
81 43 0.45
84 34 0.35
85 5 0.05
ACGTcount: A:0.15, C:0.15, G:0.13, T:0.57
Consensus pattern (82 bp):
TTTTTCTTTTGCTTTATTTTATGCTATTTGGTGTGCTGTTTTAGATGTAATTGCCCATTATCACA
TGCATTATTACCCTTTC
Found at i:1347923 original size:30 final size:30
Alignment explanation
Indices: 1347882--1347938 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
1347872 TGCATATAAA
* *
1347882 TTCTGCTAAAGACGTTGATAGATCCATGTT
1 TTCTACTAAAGACGTCGATAGATCCATGTT
1347912 TTCTACTAAAGACGTCGATAGATCCAT
1 TTCTACTAAAGACGTCGATAGATCCAT
1347939 TTCCTGTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (30 bp):
TTCTACTAAAGACGTCGATAGATCCATGTT
Found at i:1350757 original size:21 final size:21
Alignment explanation
Indices: 1350731--1350801 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
1350721 CTGTAGTAGC
*
1350731 ATCTGATATGGAAGTGGTGGT
1 ATCTGATATGGATGTGGTGGT
* *
1350752 ATCTGA-ATTGACTGTGGTGAT
1 ATCTGATATGGA-TGTGGTGGT
* *
1350773 ATCTAAAATGGATGTGGT-GT
1 ATCTGATATGGATGTGGTGGT
1350793 CATCTGATA
1 -ATCTGATA
1350802 CGACTATGGT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
20 5 0.13
21 30 0.77
22 4 0.10
ACGTcount: A:0.27, C:0.08, G:0.30, T:0.35
Consensus pattern (21 bp):
ATCTGATATGGATGTGGTGGT
Found at i:1352604 original size:23 final size:23
Alignment explanation
Indices: 1352573--1352631 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
1352563 TCAAGGGTTT
*
1352573 TATGTGGTCCTTCGGGACAAACC
1 TATGTGGTCCTTCGGGACAAAAC
* * *
1352596 TATGCGGTCCTTTGGGATAAAAC
1 TATGTGGTCCTTCGGGACAAAAC
1352619 TATGTGGTCCTTC
1 TATGTGGTCCTTC
1352632 AGAACAAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.32
Consensus pattern (23 bp):
TATGTGGTCCTTCGGGACAAAAC
Found at i:1354718 original size:21 final size:21
Alignment explanation
Indices: 1354692--1354744 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1354682 TAACAAAGGT
1354692 AGTACCGATACTCCCTATAGG
1 AGTACCGATACTCCCTATAGG
1354713 AGTACCGATACTCCCTATAGG
1 AGTACCGATACTCCCTATAGG
*
1354734 AGTACCAATAC
1 AGTACCGATAC
1354745 CTTATGTACT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (21 bp):
AGTACCGATACTCCCTATAGG
Found at i:1357946 original size:17 final size:17
Alignment explanation
Indices: 1357921--1357953 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1357911 CTAGAATGCA
*
1357921 AAAATGGTACCGATACC
1 AAAAGGGTACCGATACC
1357938 AAAAGGGTACCGATAC
1 AAAAGGGTACCGATAC
1357954 TACTTTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.21, G:0.21, T:0.15
Consensus pattern (17 bp):
AAAAGGGTACCGATACC
Found at i:1360766 original size:51 final size:50
Alignment explanation
Indices: 1360697--1360882 Score: 239
Period size: 51 Copynumber: 3.7 Consensus size: 50
1360687 ACAAAAAACA
* **
1360697 GTAACACTTAACATATACTTACACTGTTGTAAGTGAATAAAATAAACAAGT
1 GTAACACTTAACACATACTTACACTAATGTAAGTGAATAAAATAAA-AAGT
* * *
1360748 ATAACACTTAACACATACTTACACTAATGTAACTGAATAAAACAAAAAAGT
1 GTAACACTTAACACATACTTACACTAATGTAAGTGAATAAAA-TAAAAAGT
* *
1360799 GTAACACTTAACTCATACTTACAAC-AATGTAAGTAAATAAAATAAAAAGT
1 GTAACACTTAACACATACTTAC-ACTAATGTAAGTGAATAAAATAAAAAGT
* **
1360849 GTAATACTTAACACATACTTACACCGATGTAAGT
1 GTAACACTTAACACATACTTACACTAATGTAAGT
1360883 ATGCACATCT
Statistics
Matches: 118, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
49 2 0.02
50 35 0.30
51 76 0.64
52 5 0.04
ACGTcount: A:0.48, C:0.16, G:0.09, T:0.27
Consensus pattern (50 bp):
GTAACACTTAACACATACTTACACTAATGTAAGTGAATAAAATAAAAAGT
Found at i:1360808 original size:102 final size:101
Alignment explanation
Indices: 1360687--1360872 Score: 268
Period size: 102 Copynumber: 1.8 Consensus size: 101
1360677 AATTCATATT
** *
1360687 ACAAAAAACAGTAACACTTAACAT-ATACTTAC-ACTGTTGTAAGTGAATAAAATAAACAAGTAT
1 ACAAAAAACAGTAACACTTAAC-TCATACTTACAAC-AATGTAAGTAAATAAAATAAA-AAGTAT
1360750 AACACTTAACACATACTTACACTAATGTAACTGAATAAA
63 AACACTTAACACATACTTACACTAATGTAACTGAATAAA
** * *
1360789 ACAAAAAAGTGTAACACTTAACTCATACTTACAACAATGTAAGTAAATAAAATAAAAAGTGTAAT
1 ACAAAAAACAGTAACACTTAACTCATACTTACAACAATGTAAGTAAATAAAATAAAAAGTATAAC
1360854 ACTTAACACATACTTACAC
66 ACTTAACACATACTTACAC
1360873 CGATGTAAGT
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
101 27 0.36
102 46 0.61
103 2 0.03
ACGTcount: A:0.51, C:0.17, G:0.08, T:0.25
Consensus pattern (101 bp):
ACAAAAAACAGTAACACTTAACTCATACTTACAACAATGTAAGTAAATAAAATAAAAAGTATAAC
ACTTAACACATACTTACACTAATGTAACTGAATAAA
Found at i:1361025 original size:64 final size:64
Alignment explanation
Indices: 1360959--1361080 Score: 172
Period size: 64 Copynumber: 1.9 Consensus size: 64
1360949 TTATATTTTT
* * *
1360959 AAATAAATAAAAAATTAAAAATAATAAAAAATATATATTAAGTTATTTGTATACAAATTTTATTA
1 AAATATAT-AAAAATTAAAAATAATAAAAAAT-TATATTAAGTTATTTATATAAAAATTTTATTA
1361024 A
64 A
* * *
1361025 AAATATATAAAAATTATAAATAATAGAAACTTATATTAAGTTATTTATATAAAAAT
1 AAATATATAAAAATTAAAAATAATAAAAAATTATATTAAGTTATTTATATAAAAAT
1361081 ATAATAAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
64 23 0.46
65 20 0.40
66 7 0.14
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (64 bp):
AAATATATAAAAATTAAAAATAATAAAAAATTATATTAAGTTATTTATATAAAAATTTTATTAA
Found at i:1362393 original size:21 final size:21
Alignment explanation
Indices: 1362342--1362394 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
1362332 ATAATGACTA
1362342 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
1362363 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
1362384 TCGCAATGCGA
1 TCGCAATGCGA
1362395 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:1362408 original size:82 final size:81
Alignment explanation
Indices: 1362322--1362519 Score: 200
Period size: 82 Copynumber: 2.4 Consensus size: 81
1362312 GTTTCCAGAT
* * ** *
1362322 TCGCAACGCG-ATAATGACTATCGCAATGCGATTTTCCAATTTCGCGTTGCGATTTTCCCAATTC
1 TCGCAATGCGAAT-ATGACTATCGCAATGCGATTTT-CAATATCGCAATGCAATTTTCCCAATTC
1362386 GCAATGCGAATAAGTAAA
64 GCAATGCGAATAAGTAAA
* ** ** * * *
1362404 TCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTATCGCAATGCAATTTTCCTAATTCG
1 TCGCAATGCGAATAT-GACTATCGCAATGCGATTTTCAATATCGCAATGCAATTTTCCCAATTCG
* *
1362469 CATTGCGAATACGTAAA
65 CAATGCGAATAAGTAAA
* * *
1362486 TCGCAATGTGAATCTTACTATCGCAATGCGATTT
1 TCGCAATGCGAATATGACTATCGCAATGCGATTT
1362520 ACATAGCGCC
Statistics
Matches: 92, Mismatches: 22, Indels: 5
0.77 0.18 0.04
Matches are distributed among these distances:
81 14 0.15
82 60 0.65
83 18 0.20
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (81 bp):
TCGCAATGCGAATATGACTATCGCAATGCGATTTTCAATATCGCAATGCAATTTTCCCAATTCGC
AATGCGAATAAGTAAA
Found at i:1362409 original size:20 final size:21
Alignment explanation
Indices: 1362384--1362435 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1362374 TTTTCCCAAT
*
1362384 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
1362404 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1362425 TCGCAATGCGA
1 TCGCAATGCGA
1362436 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1362414 original size:41 final size:41
Alignment explanation
Indices: 1362369--1362493 Score: 119
Period size: 41 Copynumber: 3.0 Consensus size: 41
1362359 AATTTCGCGT
*
1362369 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGATTTTCCAAATTCGCAATGCGAATAAGTAAATCGCAA
* ** * * *
1362410 TGCGAATTTGGAAAATCGCAATGCG-AT-ACTGACTATCGCAA
1 TGCGATTTTCCAAATTCGCAATGCGAATAAGT-A-AATCGCAA
* * * *
1362451 TGCAATTTTCCTAATTCGCATTGCGAATACGTAAATCGCAA
1 TGCGATTTTCCAAATTCGCAATGCGAATAAGTAAATCGCAA
1362492 TG
1 TG
1362494 TGAATCTTAC
Statistics
Matches: 63, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
39 2 0.03
40 3 0.05
41 54 0.86
42 3 0.05
43 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (41 bp):
TGCGATTTTCCAAATTCGCAATGCGAATAAGTAAATCGCAA
Found at i:1363120 original size:19 final size:19
Alignment explanation
Indices: 1363098--1363143 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
1363088 AAAAATCGCA
1363098 TTGCGATTTTCATTTCACG
1 TTGCGATTTTCATTTCACG
*
1363117 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCACG
1363136 TTGCGATT
1 TTGCGATT
1363144 CTCTCGTTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCACG
Found at i:1363163 original size:33 final size:33
Alignment explanation
Indices: 1363115--1363213 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
1363105 TTTCATTTCA
**
1363115 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
*
1363148 CGTTGCGATAGTCATTTCGTGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
* *
1363181 CATTGCGATAGTCATTTCCGCGTTGCGGTTCTC
1 CGTTGCGATAGTCATTT-CGCGTTGCGATTCTC
1363214 ATTATCTCGT
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 46 0.78
34 13 0.22
ACGTcount: A:0.11, C:0.24, G:0.23, T:0.41
Consensus pattern (33 bp):
CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
Found at i:1363215 original size:20 final size:20
Alignment explanation
Indices: 1363192--1363238 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
1363182 ATTGCGATAG
*
1363192 TCATTTCCGCGTTGCGGTTC
1 TCATTTCCGCGTTGCGATTC
* *
1363212 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCGATTC
1363232 TCATTTC
1 TCATTTC
1363239 AACCAAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 1 0.05
20 20 0.91
21 1 0.05
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCGATTC
Found at i:1364566 original size:21 final size:20
Alignment explanation
Indices: 1364495--1364567 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
1364485 CTCCACTTCG
1364495 AGAGCCATCACCTCAC--CC
1 AGAGCCATCACCTCACAACC
*
1364513 AGAGCCATCACCTGATCAACC
1 AGAGCCATCACCTCA-CAACC
* * *
1364534 CGA-CTATACACCTCTACAACG
1 AGAGCCAT-CACCTC-ACAACC
1364555 AGAGCCATCACCT
1 AGAGCCATCACCT
1364568 ATCCCATCAC
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
18 14 0.33
19 1 0.02
20 3 0.07
21 20 0.48
22 4 0.10
ACGTcount: A:0.32, C:0.41, G:0.12, T:0.15
Consensus pattern (20 bp):
AGAGCCATCACCTCACAACC
Found at i:1365407 original size:21 final size:21
Alignment explanation
Indices: 1365383--1365449 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1365373 TCATTCCTCG
1365383 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1365404 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1365425 AGAGAT-CCCTCCCACCATTCA
1 AGAG-TCCCCTCCCACCGTTCA
1365446 AGAG
1 AGAG
1365450 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1365407 original size:42 final size:42
Alignment explanation
Indices: 1365331--1365449 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
1365321 GACTCGCCTG
* * * * * * *
1365331 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
1365373 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
1365415 TCA-TCGTTGAAGAGAT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGAG-TCCCCTCCCACCGTTCAAGAG
1365450 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 59 0.92
43 1 0.02
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:1368013 original size:20 final size:20
Alignment explanation
Indices: 1367986--1368039 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1367976 GAAACTTAAA
1367986 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* * *
1368006 ATCTCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGACT
*
1368026 ATCGCAATGCGAAA
1 ATCGCAACGCGAAA
1368040 TGCAAATCGC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1368048 original size:19 final size:17
Alignment explanation
Indices: 1368026--1368116 Score: 68
Period size: 14 Copynumber: 5.4 Consensus size: 17
1368016 GGAAATGGCT
1368026 ATCGCAATGCGAAATGCAA
1 ATCGCAATGCGAAAT--AA
*
1368045 ATCGCAA--CGACA-AA
1 ATCGCAATGCGAAATAA
1368059 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAAT--AA
*
1368078 ATCGCAA--CGACA-AA
1 ATCGCAATGCGAAATAA
*
1368092 ATCGTAATGCGAAATCAA
1 ATCGCAATGCGAAAT-AA
1368110 ATCGCAA
1 ATCGCAA
1368117 CGACAAAATC
Statistics
Matches: 57, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
14 17 0.30
16 8 0.14
17 8 0.14
18 8 0.14
19 16 0.28
ACGTcount: A:0.46, C:0.22, G:0.18, T:0.14
Consensus pattern (17 bp):
ATCGCAATGCGAAATAA
Found at i:1368068 original size:33 final size:33
Alignment explanation
Indices: 1368026--1368148 Score: 185
Period size: 33 Copynumber: 3.8 Consensus size: 33
1368016 GGAAATGGCT
1368026 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
*
1368059 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
*
1368092 ATCGTAATGCGAAAT-CAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
* * **
1368124 ATCGCAACGCAAAACACAAATCGCA
1 ATCGCAATGCGAAATGCAAATCGCA
1368149 TTGCGACTTT
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
32 27 0.33
33 55 0.67
ACGTcount: A:0.47, C:0.24, G:0.16, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGCAAATCGCAACGACAAA
Found at i:1368137 original size:13 final size:14
Alignment explanation
Indices: 1368043--1368137 Score: 75
Period size: 14 Copynumber: 6.2 Consensus size: 14
1368033 TGCGAAATGC
1368043 AAATCGCAACGACA
1 AAATCGCAACGACA
*
1368057 AAATCGCAATGCGAAATGA
1 AAATCGCAA--CG--A-CA
1368076 AAATCGCAACGACA
1 AAATCGCAACGACA
* *
1368090 AAATCGTAATGCGAAA
1 AAATCGCAA--CGACA
1368106 TCAAATCGCAACGACA
1 --AAATCGCAACGACA
1368122 AAATCGCAACG-CA
1 AAATCGCAACGACA
1368135 AAA
1 AAA
1368138 CACAAATCGC
Statistics
Matches: 66, Mismatches: 6, Indels: 19
0.73 0.07 0.21
Matches are distributed among these distances:
13 5 0.08
14 29 0.44
15 1 0.02
16 10 0.15
17 2 0.03
18 9 0.14
19 10 0.15
ACGTcount: A:0.49, C:0.23, G:0.16, T:0.12
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:1368145 original size:65 final size:66
Alignment explanation
Indices: 1368026--1368148 Score: 187
Period size: 65 Copynumber: 1.9 Consensus size: 66
1368016 GGAAATGGCT
* **
1368026 ATCGCAATGCGAAATGCAAATCGCAACGACAAAATCGCAATGCGAAATGAAAATCGCAACGACAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAAATCGCAACGCGAAAACAAAATCGCAACGACAA
1368091 A
66 A
*
1368092 ATCGTAATGCGAAAT-CAAATCGCAACGACAAAATCGCAACGC-AAAACACAAATCGCA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAAATCGCAACGCGAAAACA-AAATCGCA
1368149 TTGCGACTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
64 4 0.08
65 34 0.65
66 14 0.27
ACGTcount: A:0.47, C:0.24, G:0.16, T:0.12
Consensus pattern (66 bp):
ATCGCAATGCGAAATGCAAATCGCAACGACAAAATCGCAACGCGAAAACAAAATCGCAACGACAA
A
Found at i:1368166 original size:19 final size:18
Alignment explanation
Indices: 1368144--1368240 Score: 75
Period size: 19 Copynumber: 5.7 Consensus size: 18
1368134 AAAACACAAA
1368144 TCGCATTGCGACTTTCATT
1 TCGCATTGCGA-TTTCATT
* *
1368163 TCGCATTGAGATTT--TG
1 TCGCATTGCGATTTCATT
1368179 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
*
1368196 TCGCATTGCGATTT--TG
1 TCGCATTGCGATTTCATT
*
1368212 T--CTTTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
1368229 TCGCATTGCGAT
1 TCGCATTGCGAT
1368241 AGTCATTTTC
Statistics
Matches: 60, Mismatches: 8, Indels: 21
0.67 0.09 0.24
Matches are distributed among these distances:
14 12 0.20
15 6 0.10
16 6 0.10
17 6 0.10
18 7 0.12
19 23 0.38
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.46
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:1368237 original size:33 final size:33
Alignment explanation
Indices: 1368149--1368240 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
1368139 ACAAATCGCA
* *
1368149 TTGCGACTTTCATTTCGCATTGAGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
1368182 TTGCGATTTTCATTTCGCATTGCGATTTTGTCT
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1368215 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1368241 AGTCATTTTC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.14, C:0.18, G:0.20, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1368768 original size:18 final size:18
Alignment explanation
Indices: 1368742--1368786 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1368732 GTCGATCAGA
*
1368742 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1368760 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1368778 TGATGGCTC
1 TGATGGCTC
1368787 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1370154 original size:20 final size:20
Alignment explanation
Indices: 1370106--1370164 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1370096 AATAGTTTCT
**
1370106 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACAC
*
1370126 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACAC
**
1370146 GAATTTGACTATCGCAACA
1 GAAAATGACTATCGCAACA
1370165 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACAC
Found at i:1370448 original size:22 final size:22
Alignment explanation
Indices: 1370421--1370464 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1370411 GATGGAGATA
1370421 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
1370443 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
1370465 TGAGAGAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:1370741 original size:20 final size:20
Alignment explanation
Indices: 1370632--1370766 Score: 94
Period size: 20 Copynumber: 6.7 Consensus size: 20
1370622 CGCTTTGAAA
*
1370632 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTAAGT
* * * *
1370653 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTAAGT
* * *
1370673 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* * * *
1370693 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTAAGT
1370714 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* *
1370734 ATCTCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTAAGT
1370754 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1370767 TTTCCCAATT
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
19 5 0.05
20 64 0.68
21 23 0.24
22 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:1370744 original size:61 final size:61
Alignment explanation
Indices: 1370632--1370769 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
1370622 CGCTTTGAAA
* * * *
1370632 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * * *
1370693 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCTCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
1370754 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
1370770 CCCAATTCGC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:1370785 original size:61 final size:61
Alignment explanation
Indices: 1370632--1370787 Score: 152
Period size: 61 Copynumber: 2.6 Consensus size: 61
1370622 CGCTTTGAAA
* ** * * * *
1370632 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
* * ** * * * * *
1370693 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCTCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
1370754 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
1370788 TTACTTATTC
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
61 76 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:1370877 original size:21 final size:21
Alignment explanation
Indices: 1370837--1370877 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1370827 ACTGTATACC
** *
1370837 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
1370858 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
1370878 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:1376137 original size:64 final size:64
Alignment explanation
Indices: 1376053--1376278 Score: 248
Period size: 64 Copynumber: 3.5 Consensus size: 64
1376043 TTGAAGGTGT
* * *
1376053 ATCGATGCATAGGTAGTGCATCGATGCA-CTCTTTTAAAATACAAACATCAAATGCAATTAGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCTTTT-AAATACAAACATCGAATGCAATTAGTGC
** * * *
1376117 ATCGATGCATAAGTCA-TGCATCGATGCATCCCAGTGATAATAC-AACATCGAATGTAATTCGTG
1 ATCGATGCATAAGT-AGTGCATCGATGCATCCCTTTTA-AATACAAACATCGAATGCAATTAGTG
1376180 C
64 C
* *
1376181 ATCGATGCATAAGTAGTGCATCGATGCATCCCGTTATT-AAT-GAAACATCGAATGCATTTTA-T
1 ATCGATGCATAAGTAGTGCATCGATGCATCCC-TT-TTAAATACAAACATCGAATGCA-ATTAGT
1376243 GC
63 GC
* *
1376245 ATCGATGCACAAGTAGTGCATCGATGCATACCTT
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCTT
1376279 CATTAAAAGA
Statistics
Matches: 137, Mismatches: 17, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
63 3 0.02
64 122 0.89
65 11 0.08
66 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCTTTTAAATACAAACATCGAATGCAATTAGTGC
Found at i:1376984 original size:30 final size:30
Alignment explanation
Indices: 1376948--1377011 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
1376938 AAGGAACATA
* *
1376948 TGGATAGTTGCCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* * *
1376978 TGGATAGTTACCGGGGTTCTTTGTAACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
1377008 TGGA
1 TGGA
1377012 CAGGTCCTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:1380288 original size:64 final size:64
Alignment explanation
Indices: 1380204--1380429 Score: 257
Period size: 64 Copynumber: 3.5 Consensus size: 64
1380194 TTGAAGATGT
* *
1380204 ATCGATGCATAGGTAGTGCATCGATGCA-CTCTTTTAAAATACAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCTTTT-AAATACAAACATCGAATGCAATTAGTGC
** * * *
1380268 ATCGATGCATAAGTCA-TGCATCGATGCATCCCAGTGATAATAC-AACATCGAATGTAATTCGTG
1 ATCGATGCATAAGT-AGTGCATCGATGCATCCCTTTTA-AATACAAACATCGAATGCAATTAGTG
1380331 C
64 C
* *
1380332 ATCGATGCATAAGTAGTGCATCGATGCATCCCGTTATT-AAT-GAAACATCGAATGCATTTTA-T
1 ATCGATGCATAAGTAGTGCATCGATGCATCCC-TT-TTAAATACAAACATCGAATGCA-ATTAGT
1380394 GC
63 GC
* *
1380396 ATCGATGCACAAGTAGTGCATCGATGCATACCTT
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCTT
1380430 CATTAAAAGA
Statistics
Matches: 138, Mismatches: 16, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
63 3 0.02
64 123 0.89
65 11 0.08
66 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCTTTTAAATACAAACATCGAATGCAATTAGTGC
Found at i:1381155 original size:30 final size:30
Alignment explanation
Indices: 1381104--1381164 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1381094 AAGGAACATA
* *
1381104 TGGATAGTTGCCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* * *
1381134 TGGATAGTTACCGGGGTTCTTTGTAACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
1381164 T
1 T
1381165 AGACAGGTCC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:1391426 original size:125 final size:122
Alignment explanation
Indices: 1391237--1391483 Score: 359
Period size: 125 Copynumber: 2.0 Consensus size: 122
1391227 AGATGAATCT
* * * *
1391237 CAATACACATTTATTTATCCCAAATTTTGTTTGAACATAAAGCATGTGTGGATATTCAACAAAGA
1 CAATAAACATTTATTTATCCCAAATTTTGATTGAACATAAAGCATGTGTCGATACTCAACAAAGA
* * * *
1391302 AAGATGCAAAATGATTATTCAGGAAAACTAAAATATGTGTGCAACTGTTTCCAATTC
66 AAGATACAAAATGATTATTCAGGAAAACCAAAAGATATGTGCAACTGTTTCCAATTC
**
1391359 CAATAAACATTTATTTATCCCGGATTTTGATTGACCAACATAAAGCATGTGTCGATACTCAACAA
1 CAATAAACATTTATTTATCCCAAATTTTGATTG---AACATAAAGCATGTGTCGATACTCAACAA
* *
1391424 AGAAAGATACAAAATGATTATTCAGGAAAACCAAAAGATATGTGCAATTTTTTCCAATTC
63 AGAAAGATACAAAATGATTATTCAGGAAAACCAAAAGATATGTGCAACTGTTTCCAATTC
1391484 AACATATTTT
Statistics
Matches: 110, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
122 29 0.26
125 81 0.74
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (122 bp):
CAATAAACATTTATTTATCCCAAATTTTGATTGAACATAAAGCATGTGTCGATACTCAACAAAGA
AAGATACAAAATGATTATTCAGGAAAACCAAAAGATATGTGCAACTGTTTCCAATTC
Found at i:1393898 original size:17 final size:17
Alignment explanation
Indices: 1393876--1393910 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1393866 TATCCATAGA
1393876 TTGTATGAAGTTAGAAG
1 TTGTATGAAGTTAGAAG
1393893 TTGTATGAAGTTAGAAG
1 TTGTATGAAGTTAGAAG
1393910 T
1 T
1393911 GTTTGTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (17 bp):
TTGTATGAAGTTAGAAG
Found at i:1395527 original size:32 final size:32
Alignment explanation
Indices: 1395489--1395553 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
1395479 TAAATCAGAT
1395489 TAAATTAGATATCGA-GTCAGATCAATATCAAA
1 TAAATTA-ATATCGAGGTCAGATCAATATCAAA
* ** *
1395521 TAAATTAATCTTTAGGTCATATCAATATCAAA
1 TAAATTAATATCGAGGTCAGATCAATATCAAA
1395553 T
1 T
1395554 TGATTAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 4 0.14
32 24 0.86
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (32 bp):
TAAATTAATATCGAGGTCAGATCAATATCAAA
Found at i:1395560 original size:32 final size:32
Alignment explanation
Indices: 1395504--1395567 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
1395494 TAGATATCGA
1395504 GTCAGATCAATATCAAATAAATTAATCTTTAG
1 GTCAGATCAATATCAAATAAATTAATCTTTAG
* ** *
1395536 GTCATATCAATATCAAATTGATTAATTTTTAG
1 GTCAGATCAATATCAAATAAATTAATCTTTAG
1395568 TTTGAAGCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (32 bp):
GTCAGATCAATATCAAATAAATTAATCTTTAG
Found at i:1395673 original size:32 final size:31
Alignment explanation
Indices: 1395509--1395676 Score: 83
Period size: 32 Copynumber: 5.3 Consensus size: 31
1395499 ATCGAGTCAG
* * *
1395509 ATCAATATCAAATAAATTAATCTTTAGGTCA
1 ATCAATATCAAATCAATTAATTTTTAGATCA
** * *
1395540 TATCAATATCAAATTGATTAATTTTTAGTTTGA
1 -ATCAATATCAAATCAATTAATTTTTAG-ATCA
* * *
1395573 AGCAATAGT-AGATCAA-T-ATCTTTTCAAATCGA
1 ATCAATA-TCAAATCAATTAAT-TTTT-AGATC-A
* ** * *
1395605 GTCAATATTGAATCGATTGACTTTTTA-ATCGA
1 ATCAATATCAAATCAATT-AATTTTTAGATC-A
*
1395637 ATCAATATCAAATCAATTAATTTTTAGTTCA
1 ATCAATATCAAATCAATTAATTTTTAGATCA
1395668 TATCAATAT
1 -ATCAATAT
1395677 TTGGATCTTC
Statistics
Matches: 101, Mismatches: 24, Indels: 22
0.69 0.16 0.15
Matches are distributed among these distances:
30 2 0.02
31 15 0.15
32 74 0.73
33 5 0.05
34 4 0.04
35 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (31 bp):
ATCAATATCAAATCAATTAATTTTTAGATCA
Found at i:1396830 original size:17 final size:17
Alignment explanation
Indices: 1396796--1396828 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1396786 GTTAGGGGTA
1396796 AGGGATTTAGGATTTTT
1 AGGGATTTAGGATTTTT
1396813 AGGGATTTA-GATTTTT
1 AGGGATTTAGGATTTTT
1396829 TATTGTAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.48
Consensus pattern (17 bp):
AGGGATTTAGGATTTTT
Found at i:1398208 original size:17 final size:18
Alignment explanation
Indices: 1398182--1398227 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
1398172 TCAGATTCAC
*
1398182 ATTCCAATTCC-TGACAG
1 ATTCCAATTCCTTCACAG
*
1398199 ATTTCAATTCCTTCACAG
1 ATTCCAATTCCTTCACAG
1398217 ATTCCAATTCC
1 ATTCCAATTCC
1398228 CTCAGAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.28, C:0.30, G:0.07, T:0.35
Consensus pattern (18 bp):
ATTCCAATTCCTTCACAG
Found at i:1404258 original size:12 final size:13
Alignment explanation
Indices: 1404238--1404269 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
1404228 ACCCGTTTTC
1404238 TTATATTTTTATT
1 TTATATTTTTATT
1404251 TT-TATTTTTATT
1 TTATATTTTTATT
1404263 TTATATT
1 TTATATT
1404270 AATTTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TTATATTTTTATT
Found at i:1413264 original size:84 final size:84
Alignment explanation
Indices: 1413123--1413317 Score: 372
Period size: 84 Copynumber: 2.3 Consensus size: 84
1413113 TTCTCCTTGC
* *
1413123 AGATATTAATCAAGTTAAATTATCCCTATAATTGGTTGATTTCCACACCGCTGTCTTTTCTATGT
1 AGATATTAACCAAGTTAAACTATCCCTATAATTGGTTGATTTCCACACCGCTGTCTTTTCTATGT
1413188 TGCCTTGAGTTTAGAGTTT
66 TGCCTTGAGTTTAGAGTTT
1413207 AGATATTAACCAAGTTAAACTATCCCTATAATTGGTTGATTTCCACACCGCTGTCTTTTCTATGT
1 AGATATTAACCAAGTTAAACTATCCCTATAATTGGTTGATTTCCACACCGCTGTCTTTTCTATGT
1413272 TGCCTTGAGTTTAGAGTTT
66 TGCCTTGAGTTTAGAGTTT
1413291 AGATATTAACCAAGTTAAACTATCCCT
1 AGATATTAACCAAGTTAAACTATCCCT
1413318 TGATACATTT
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 109 1.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.40
Consensus pattern (84 bp):
AGATATTAACCAAGTTAAACTATCCCTATAATTGGTTGATTTCCACACCGCTGTCTTTTCTATGT
TGCCTTGAGTTTAGAGTTT
Found at i:1415276 original size:60 final size:60
Alignment explanation
Indices: 1415139--1415276 Score: 143
Period size: 60 Copynumber: 2.3 Consensus size: 60
1415129 AACATAATAA
* * **
1415139 ATAGTCGGGTGACCATTTTTTAACTTTTAATAATAGAGGGACTTAACAAAGCAACACTTT
1 ATAGTCGGGTGACCATTTTGTAACTTTTAATAATAGAGAGACTTAACAAAGCAACACTCC
* *** * * * * *
1415199 ATAGTTGAACGATCATTTTGTAACTTTTAATAGTCGAGAGACTTAATAAAGCAATA-TCCC
1 ATAGTCGGGTGACCATTTTGTAACTTTTAATAATAGAGAGACTTAACAAAGCAACACT-CC
1415259 ATAGTCGGGTGACCATTT
1 ATAGTCGGGTGACCATTT
1415277 GCGTTCTTTA
Statistics
Matches: 59, Mismatches: 18, Indels: 2
0.75 0.23 0.03
Matches are distributed among these distances:
59 1 0.02
60 58 0.98
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Consensus pattern (60 bp):
ATAGTCGGGTGACCATTTTGTAACTTTTAATAATAGAGAGACTTAACAAAGCAACACTCC
Found at i:1416209 original size:19 final size:19
Alignment explanation
Indices: 1416185--1416221 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1416175 ATGACCAACA
*
1416185 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
1416204 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
1416222 CAGTATCGCA
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:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:1416327 original size:20 final size:20
Alignment explanation
Indices: 1416302--1416366 Score: 121
Period size: 20 Copynumber: 3.2 Consensus size: 20
1416292 GTTGCGATTT
1416302 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
1416322 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
*
1416342 TCGCAATGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
1416362 TCGCA
1 TCGCA
1416367 TTGCGATAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:1416554 original size:24 final size:23
Alignment explanation
Indices: 1416527--1416590 Score: 80
Period size: 22 Copynumber: 2.8 Consensus size: 23
1416517 CATCTCTCAC
1416527 TCTCTACGAC-AACATCCGTCCCCA
1 TCTCT-CGACGAA-ATCCGTCCCCA
1416551 TCTC-CGACGAAATCCGTCCCCA
1 TCTCTCGACGAAATCCGTCCCCA
*
1416573 TCTCT-GATGAAATCCGTC
1 TCTCTCGACGAAATCCGTC
1416591 TATCTCCATC
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
22 31 0.84
23 2 0.05
24 4 0.11
ACGTcount: A:0.23, C:0.41, G:0.12, T:0.23
Consensus pattern (23 bp):
TCTCTCGACGAAATCCGTCCCCA
Found at i:1416558 original size:22 final size:22
Alignment explanation
Indices: 1416540--1416590 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
1416530 CTACGACAAC
1416540 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* *
1416562 ATCCGTCCCCATCTCTGATGAA
1 ATCCGTCCCCATCTCCGACGAA
1416584 ATCCGTC
1 ATCCGTC
1416591 TATCTCCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.41, G:0.14, T:0.24
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:1417051 original size:20 final size:20
Alignment explanation
Indices: 1416998--1417053 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1416988 GATAGTCAAA
* **
1416998 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
*
1417018 TTCATGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
1417038 TTCGTGTTGCGATTTT
1 TTCGTGTTGCGATTTT
1417054 AAGTTTCAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.12, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:1417060 original size:20 final size:20
Alignment explanation
Indices: 1417017--1417061 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1417007 CGATAGTCAT
* *
1417017 TTTCATGTTGCGATTTTCAT
1 TTTCATGTTGCGATTTTAAG
*
1417037 TTTCGTGTTGCGATTTTAAG
1 TTTCATGTTGCGATTTTAAG
1417057 TTTCA
1 TTTCA
1417062 GAAACTATTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.13, G:0.18, T:0.53
Consensus pattern (20 bp):
TTTCATGTTGCGATTTTAAG
Found at i:1418986 original size:20 final size:20
Alignment explanation
Indices: 1418961--1419006 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1418951 CGAAACTAAA
*
1418961 ATCGCAACGCGTAAATGACT
1 ATCGCAACGCGGAAATGACT
1418981 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
1419001 ATCGCA
1 ATCGCA
1419007 TTGCGATAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:1419046 original size:20 final size:20
Alignment explanation
Indices: 1419007--1419073 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
1418997 GACTATCGCA
*
1419007 TTGCGATAGTCAAATT-CGCG
1 TTGCGATAGTC-ATTTCCGCG
*
1419027 TTGCGATGGTCATTTCCGCG
1 TTGCGATAGTCATTTCCGCG
* *
1419047 TTGTGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTCCGCG
1419067 TTGCGAT
1 TTGCGAT
1419074 TTTAAGTTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
19 3 0.08
20 37 0.93
ACGTcount: A:0.16, C:0.19, G:0.27, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGCG
Found at i:1419083 original size:20 final size:20
Alignment explanation
Indices: 1419060--1419103 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1419050 TGATAGTCAT
1419060 TTTCGCGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
*
1419080 TTTCGTGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
1419100 TTTC
1 TTTC
1419104 AGAAACTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTAAG
Found at i:1419664 original size:21 final size:21
Alignment explanation
Indices: 1419578--1419657 Score: 106
Period size: 21 Copynumber: 3.8 Consensus size: 21
1419568 GCCCGACTCA
1419578 CCTGTCATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* ** *
1419599 CCTATCATCCCTCAAGAGTCC
1 CCTGTCATCGTTCAAGAGGCC
*
1419620 CCTCTCATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
*
1419641 CCTGTCATCGTTGAAGA
1 CCTGTCATCGTTCAAGA
1419658 TGTCCCTCCC
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.21, C:0.35, G:0.19, T:0.25
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:1419676 original size:42 final size:42
Alignment explanation
Indices: 1419588--1419679 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
1419578 CCTGTCATCG
* * *
1419588 TTCAAGAGGCCCCTATCATCCCTCAAGAGTCCCCTCTCATCG
1 TTCAAGAGGCCCCTATCATCCCTCAAGAGTCCCCTCCCACCA
* ** *
1419630 TTCAAGAGGCCCCTGTCATCGTTGAAGATGT-CCCTCCCACCA
1 TTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCACCA
1419672 TTCAAGAG
1 TTCAAGAG
1419680 CTCGATTCAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 40 0.95
43 2 0.05
ACGTcount: A:0.23, C:0.36, G:0.17, T:0.24
Consensus pattern (42 bp):
TTCAAGAGGCCCCTATCATCCCTCAAGAGTCCCCTCCCACCA
Found at i:1421083 original size:14 final size:14
Alignment explanation
Indices: 1421064--1421113 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
1421054 GCTTGTTTAA
1421064 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
**
1421078 TTGATTTGTTTAA-
1 TTGATTTGTAAAAG
*
1421091 TTGATTTGTAAGAG
1 TTGATTTGTAAAAG
1421105 TTGATTTGT
1 TTGATTTGT
1421114 TTAATCGATT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
13 10 0.33
14 20 0.67
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:1421086 original size:27 final size:27
Alignment explanation
Indices: 1421056--1421145 Score: 126
Period size: 27 Copynumber: 3.2 Consensus size: 27
1421046 CATTTTTTGC
1421056 TTGTTTAATTGATTTGTAAAAGTTGAT
1 TTGTTTAATTGATTTGTAAAAGTTGAT
*
1421083 TTGTTTAATTGATTTGTAAGAGTTGAT
1 TTGTTTAATTGATTTGTAAAAGTTGAT
*
1421110 TTGTTTAATCGATTGAAATGTAAAAGTTGAT
1 TTGTTTAATTGATT----TGTAAAAGTTGAT
1421141 TTGTT
1 TTGTT
1421146 GATTTCAATC
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
27 39 0.70
31 17 0.30
ACGTcount: A:0.29, C:0.01, G:0.20, T:0.50
Consensus pattern (27 bp):
TTGTTTAATTGATTTGTAAAAGTTGAT
Found at i:1421096 original size:13 final size:13
Alignment explanation
Indices: 1421056--1421123 Score: 66
Period size: 13 Copynumber: 5.1 Consensus size: 13
1421046 CATTTTTTGC
1421056 TTGTTTAATTGAT
1 TTGTTTAATTGAT
**
1421069 TTGTAAAAGTTGAT
1 TTGTTTAA-TTGAT
1421083 TTGTTTAATTGAT
1 TTGTTTAATTGAT
*
1421096 TTG-TAAGAGTTGAT
1 TTGTTTA-A-TTGAT
*
1421110 TTGTTTAATCGAT
1 TTGTTTAATTGAT
1421123 T
1 T
1421124 GAAATGTAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
12 2 0.05
13 20 0.45
14 20 0.45
15 2 0.05
ACGTcount: A:0.26, C:0.01, G:0.19, T:0.53
Consensus pattern (13 bp):
TTGTTTAATTGAT
Found at i:1421250 original size:20 final size:20
Alignment explanation
Indices: 1421212--1421250 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1421202 ATGGTAAACT
*
1421212 CAAAATCGCAATGCAAAAGC
1 CAAAATCGCAACGCAAAAGC
*
1421232 CAAAATCGCAACGCGAAAG
1 CAAAATCGCAACGCAAAAG
1421251 TCAATTCGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.26, G:0.18, T:0.08
Consensus pattern (20 bp):
CAAAATCGCAACGCAAAAGC
Found at i:1421318 original size:20 final size:20
Alignment explanation
Indices: 1421293--1421423 Score: 130
Period size: 20 Copynumber: 6.8 Consensus size: 20
1421283 GCGATTTTCT
*
1421293 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
*
1421313 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
1421333 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* **
1421353 CATTGCGAT--T----TTTT
1 CGTTGCGATAGTCAAATTCG
* *
1421367 CGTTACGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
1421387 CGTTGCGATAGTAAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
1421407 CGTTGCAATATTCAAAT
1 CGTTGCGATAGTCAAAT
1421424 GAATGTGTAA
Statistics
Matches: 89, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
14 9 0.10
16 1 0.01
18 1 0.01
20 78 0.88
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1421319 original size:34 final size:34
Alignment explanation
Indices: 1421259--1421395 Score: 130
Period size: 34 Copynumber: 3.9 Consensus size: 34
1421249 AGTCAATTCG
* ** *
1421259 CGTTGCGATAGTCTAATAAGCTTTGCGATTTTCT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
* *
1421293 CGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGAT--T----TTCT
* *
1421333 CGTTGCGATAGTCAAATTCGCATTGCGATTTTTT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
* *
1421367 CGTTACGATAGTCATATTCGCGTTGCGAT
1 CGTTGCGATAGTCAAATTCGCGTTGCGAT
1421396 AGTAAAATTC
Statistics
Matches: 84, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
34 52 0.62
36 1 0.01
38 1 0.01
40 30 0.36
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
Found at i:1421376 original size:74 final size:74
Alignment explanation
Indices: 1421253--1421423 Score: 234
Period size: 74 Copynumber: 2.3 Consensus size: 74
1421243 CGCGAAAGTC
* * *
1421253 AATTCGCGTTGCGATAGTCTAATAAGCTTTGCGATTTTCTCGTTGCGATAGTCAAATTCCCGTTG
1 AATTCGCGTTGCGATAGTCAAATAAGCATTGCGATTTTCTCGTTACGATAGTCAAATTCCCGTTG
*
1421318 CGATAATCA
66 CGATAATAA
** * * *
1421327 AATTCGCGTTGCGATAGTCAAATTCGCATTGCGATTTTTTCGTTACGATAGTCATATTCGCGTTG
1 AATTCGCGTTGCGATAGTCAAATAAGCATTGCGATTTTCTCGTTACGATAGTCAAATTCCCGTTG
*
1421392 CGATAGTAA
66 CGATAATAA
* *
1421401 AATTCGCGTTGCAATATTCAAAT
1 AATTCGCGTTGCGATAGTCAAAT
1421424 GAATGTGTAA
Statistics
Matches: 85, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
74 85 1.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.36
Consensus pattern (74 bp):
AATTCGCGTTGCGATAGTCAAATAAGCATTGCGATTTTCTCGTTACGATAGTCAAATTCCCGTTG
CGATAATAA
Found at i:1421646 original size:140 final size:140
Alignment explanation
Indices: 1421394--1421676 Score: 503
Period size: 140 Copynumber: 2.0 Consensus size: 140
1421384 TCGCGTTGCG
*
1421394 ATAGTAAAATTCGCGTTGCAATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
1 ATAGTAAAATTCGCGTTGCAATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATAA
*
1421459 TAGCAATGTTCAAACTCAAGTTATTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
1421524 AATACACATA
131 AATACACATA
* * *
1421534 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATAA
1 ATAGTAAAATTCGCGTTGCAATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATAA
*
1421599 TAGCAATGTTTAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
*
1421664 AATACATATA
131 AATACACATA
1421674 ATA
1 ATA
1421677 CAACGTTTAC
Statistics
Matches: 136, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 136 1.00
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.29
Consensus pattern (140 bp):
ATAGTAAAATTCGCGTTGCAATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATAA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:1421757 original size:18 final size:18
Alignment explanation
Indices: 1421734--1421768 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1421724 AAGCCAGTTG
*
1421734 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1421752 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
1421769 ACCTTTTTCT
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:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1424955 original size:20 final size:20
Alignment explanation
Indices: 1424906--1424955 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1424896 TTGAAATACA
* *
1424906 GCGTTGCGACAGTCAGAATC
1 GCGTTGCGATAGTCAGAACC
1424926 GCGTTGCGATAGTCAGAACC
1 GCGTTGCGATAGTCAGAACC
1424946 GCGTTGCGAT
1 GCGTTGCGAT
1424956 TATGTATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.22, C:0.24, G:0.32, T:0.22
Consensus pattern (20 bp):
GCGTTGCGATAGTCAGAACC
Found at i:1425077 original size:19 final size:19
Alignment explanation
Indices: 1425053--1425091 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1425043 TTTGCAATAC
*
1425053 TAGAGATCGCGTTGCGATT
1 TAGAGATCGCATTGCGATT
1425072 TAGAGATCGCATTGCGATT
1 TAGAGATCGCATTGCGATT
1425091 T
1 T
1425092 TGTTGGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.33
Consensus pattern (19 bp):
TAGAGATCGCATTGCGATT
Found at i:1425640 original size:20 final size:21
Alignment explanation
Indices: 1425591--1425643 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
1425581 AGGGTTTGAC
*
1425591 TAGTGGTTTAGGTTATTTTCT
1 TAGTGGTTTAGGTTATTTTCG
1425612 TAGTGGTTTAGGTTATATTT-G
1 TAGTGGTTTAGGTTAT-TTTCG
1425633 TA-TGGTTTAGG
1 TAGTGGTTTAGG
1425644 GCTTTCAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 9 0.30
21 18 0.60
22 3 0.10
ACGTcount: A:0.17, C:0.02, G:0.28, T:0.53
Consensus pattern (21 bp):
TAGTGGTTTAGGTTATTTTCG
Found at i:1431441 original size:39 final size:39
Alignment explanation
Indices: 1431395--1431471 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
1431385 TTTATATTTT
1431395 CTATTGATAATATATTTTTAGTTCTTTGAATTTTATAAA
1 CTATTGATAATATATTTTTAGTTCTTTGAATTTTATAAA
1431434 CTATTGATAATATATTTTTAGTTCTTTGAATTTTATAA
1 CTATTGATAATATATTTTTAGTTCTTTGAATTTTATAA
1431472 GTTTATGCTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (39 bp):
CTATTGATAATATATTTTTAGTTCTTTGAATTTTATAAA
Found at i:1438716 original size:19 final size:19
Alignment explanation
Indices: 1438694--1438732 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1438684 TGTTTTCTTA
1438694 AATCCTTTCTATTTTCCAT
1 AATCCTTTCTATTTTCCAT
1438713 AATCCTTTCTATTTTCCAT
1 AATCCTTTCTATTTTCCAT
1438732 A
1 A
1438733 CGAAATCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.26, G:0.00, T:0.51
Consensus pattern (19 bp):
AATCCTTTCTATTTTCCAT
Found at i:1442463 original size:29 final size:27
Alignment explanation
Indices: 1442410--1442464 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
1442400 TCCCAATTAA
*
1442410 TATTTTTTAACATCTTGATCATTTAGC
1 TATTTTTTAACATCTTAATCATTTAGC
1442437 TATTTTTTAAGTCATACTTAAT-ATTTAG
1 TATTTTTTAA--CAT-CTTAATCATTTAG
1442465 TTTTAGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 10 0.42
29 9 0.38
30 5 0.21
ACGTcount: A:0.29, C:0.11, G:0.07, T:0.53
Consensus pattern (27 bp):
TATTTTTTAACATCTTAATCATTTAGC
Found at i:1446126 original size:26 final size:29
Alignment explanation
Indices: 1446097--1446155 Score: 88
Period size: 26 Copynumber: 2.1 Consensus size: 29
1446087 GCAACATGTT
*
1446097 TTTTAATGAGC-ACGAGTCGAG-AA-AAA
1 TTTTAACGAGCAACGAGTCGAGCAACAAA
1446123 TTTTAACGAGCAACGAGTCGAGCAACAAA
1 TTTTAACGAGCAACGAGTCGAGCAACAAA
1446152 TTTT
1 TTTT
1446156 TTTAACGAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 10 0.34
27 10 0.34
28 2 0.07
29 7 0.24
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.25
Consensus pattern (29 bp):
TTTTAACGAGCAACGAGTCGAGCAACAAA
Found at i:1446161 original size:32 final size:30
Alignment explanation
Indices: 1446095--1446177 Score: 86
Period size: 31 Copynumber: 2.9 Consensus size: 30
1446085 GAGCAACATG
*
1446095 TTTTTTAATGAGC-ACGAGTCGAG-AAAAA
1 TTTTTTAACGAGCAACGAGTCGAGCAAAAA
1446123 --TTTTAACGAGCAACGAGTCGAGCAACAAA
1 TTTTTTAACGAGCAACGAGTCGAGCAA-AAA
* *
1446152 TTTTTTTAACGAG-ATCAAGTCGAGCA
1 -TTTTTTAACGAGCAACGAGTCGAGCA
1446178 CTGCCTAACT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
26 10 0.22
27 10 0.22
28 2 0.04
29 3 0.07
31 11 0.24
32 10 0.22
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (30 bp):
TTTTTTAACGAGCAACGAGTCGAGCAAAAA
Found at i:1450080 original size:59 final size:59
Alignment explanation
Indices: 1450008--1450127 Score: 240
Period size: 59 Copynumber: 2.0 Consensus size: 59
1449998 GCTTGCTTTC
1450008 GACTAAACATACCCTTGTTAATTCCCATTGAGAGTTTGTATTATCAAGAAAGCAAAAGG
1 GACTAAACATACCCTTGTTAATTCCCATTGAGAGTTTGTATTATCAAGAAAGCAAAAGG
1450067 GACTAAACATACCCTTGTTAATTCCCATTGAGAGTTTGTATTATCAAGAAAGCAAAAGG
1 GACTAAACATACCCTTGTTAATTCCCATTGAGAGTTTGTATTATCAAGAAAGCAAAAGG
1450126 GA
1 GA
1450128 AAAAAATTAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (59 bp):
GACTAAACATACCCTTGTTAATTCCCATTGAGAGTTTGTATTATCAAGAAAGCAAAAGG
Found at i:1451752 original size:29 final size:29
Alignment explanation
Indices: 1451720--1451788 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
1451710 TTGTATATAT
*
1451720 TTTTATTGCATATTAA-CTACTAACTTTTA
1 TTTTATTGCACATTAATC-ACTAACTTTTA
1451749 TTTTATTGCACATTAATCACTAACTTTTA
1 TTTTATTGCACATTAATCACTAACTTTTA
1451778 TTTTATTGCAC
1 TTTTATTGCAC
1451789 TTTTACTTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 37 0.97
30 1 0.03
ACGTcount: A:0.29, C:0.16, G:0.04, T:0.51
Consensus pattern (29 bp):
TTTTATTGCACATTAATCACTAACTTTTA
Found at i:1451911 original size:14 final size:14
Alignment explanation
Indices: 1451892--1451918 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1451882 CCACTAACTT
1451892 TTTTATTTTATTTG
1 TTTTATTTTATTTG
1451906 TTTTATTTTATTT
1 TTTTATTTTATTT
1451919 TTATTAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.04, T:0.81
Consensus pattern (14 bp):
TTTTATTTTATTTG
Found at i:1469080 original size:17 final size:17
Alignment explanation
Indices: 1469058--1469092 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1469048 GATCATAGGG
1469058 CCGAAGCATGTGTATGC
1 CCGAAGCATGTGTATGC
1469075 CCGAAGCATGTGTATGC
1 CCGAAGCATGTGTATGC
1469092 C
1 C
1469093 TTCCAGTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.26, G:0.29, T:0.23
Consensus pattern (17 bp):
CCGAAGCATGTGTATGC
Done.