Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009344.1 Hibiscus syriacus cultivar Beakdansim tig00113124_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: 4287485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 24
Found at i:1429544 original size:24 final size:24
Alignment explanation
Indices: 1429517--1429610 Score: 129
Period size: 24 Copynumber: 4.0 Consensus size: 24
1429507 GCCACATAGG
1429517 TTTGTCCCGAATGACCACGTAGAA
1 TTTGTCCCGAATGACCACGTAGAA
* *
1429541 TTTGTCCCGAATGAACTCGTAGAA
1 TTTGTCCCGAATGACCACGTAGAA
*
1429565 TTTGTCCCGAATGACCACATAG-A
1 TTTGTCCCGAATGACCACGTAGAA
* *
1429588 -TTGTCCCGAAGGACCGCGTAGAA
1 TTTGTCCCGAATGACCACGTAGAA
1429611 CCCTCGACTC
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.30
23 2 0.03
24 41 0.67
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (24 bp):
TTTGTCCCGAATGACCACGTAGAA
Found at i:1432114 original size:23 final size:26
Alignment explanation
Indices: 1432077--1432145 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
1432067 TTCTCTTGTG
1432077 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
1432101 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
* *
1432126 ATCA--CATATCATATCACATG
1 ATCATGTATCTCATATCACATG
1432146 AACATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 21 0.52
25 8 0.20
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:1432127 original size:12 final size:12
Alignment explanation
Indices: 1432110--1432145 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
1432100 TATCATGTTC
1432110 TCATATCACATG
1 TCATATCACATG
*
1432122 TCATATCACATA
1 TCATATCACATG
1432134 TCATATCACATG
1 TCATATCACATG
1432146 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:1432561 original size:64 final size:62
Alignment explanation
Indices: 1432453--1432678 Score: 231
Period size: 64 Copynumber: 3.5 Consensus size: 62
1432443 TAATGAAGGT
* ** ** *
1432453 ATGCATCGATGCACTA-CTGATGCATCGGTGCATAAAAGGTATTCGATGTATTATTATTGTTGGG
1 ATGCATCGATGCACTACCT-ATGCATCGATGCACCAATTGCATTCGATGT-TTATTATT-TTGGG
* *
1432517 ATGCATCGATGCACTCCCTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACCTATGCATCGATGCACCAATTGCATTCGATGTTT-ATTATT-TTGGG
* ** * *
1432581 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTT-TTATTTTAAAAGA
1 ATGCATCGATGCACTACCTATGCATCGATGCACCAATTGCATTCGATGTTTATTATTTT---GGG
* *
1432645 ATGCATCGATGCACTACCAATGCATCGATACACC
1 ATGCATCGATGCACTACCTATGCATCGATGCACC
1432679 TTCAAACAAT
Statistics
Matches: 136, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
61 1 0.01
62 5 0.04
63 2 0.01
64 126 0.93
65 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (62 bp):
ATGCATCGATGCACTACCTATGCATCGATGCACCAATTGCATTCGATGTTTATTATTTTGGG
Found at i:1435795 original size:22 final size:21
Alignment explanation
Indices: 1435771--1435810 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1435761 ATTAAGTTTT
* *
1435771 TTTTAAATTTAAATTTTATTA
1 TTTTAAAATAAAATTTTATTA
1435792 TTTTAAAATAAAATTTTAT
1 TTTTAAAATAAAATTTTAT
1435811 AAACATGACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTAAAATAAAATTTTATTA
Found at i:1438984 original size:2 final size:2
Alignment explanation
Indices: 1438977--1439057 Score: 153
Period size: 2 Copynumber: 40.5 Consensus size: 2
1438967 TGAATGAGTA
1438977 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1439019 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1439058 GTTTTCAAAT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1443095 original size:64 final size:64
Alignment explanation
Indices: 1442992--1443117 Score: 148
Period size: 64 Copynumber: 2.0 Consensus size: 64
1442982 ATGCACTTCT
* *
1442992 TTAAAATAAAAACATCGAATGTCATTAGTATATCAATGCACAAG-TAGTGCATCGATGCACCCCC
1 TTAAAATAAAAACATCGAATGACATTAGTATACCAATGCA-AAGATAGTGCATCGATGCACCCCC
* * * * * *
1443056 TTAAAATATAAACATCGAATGAGATTTA-TGTACCGATGCATAGATTGTGCATCGATGCACCC
1 TTAAAATAAAAACATCGAATGACA-TTAGTATACCAATGCAAAGATAGTGCATCGATGCACCC
1443118 GTCAAGGGAT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
63 2 0.04
64 47 0.90
65 3 0.06
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (64 bp):
TTAAAATAAAAACATCGAATGACATTAGTATACCAATGCAAAGATAGTGCATCGATGCACCCCC
Found at i:1443719 original size:38 final size:38
Alignment explanation
Indices: 1443666--1443761 Score: 99
Period size: 38 Copynumber: 2.5 Consensus size: 38
1443656 TCGAGGGATT
*
1443666 ATCAGTGGTCCTTCGGGACAT-AGTGGT-TCTTCGAAAC
1 ATCAGTGGTCATTCGGGACATCAGTGGTCT-TTCGAAAC
* **
1443703 AATCAGTGGTCATTCGGAACAATCAGTGGTCTTTCGGGAC
1 -ATCAGTGGTCATTCGGGAC-ATCAGTGGTCTTTCGAAAC
*
1443743 AT-AGTGGTCATTCGAGACA
1 ATCAGTGGTCATTCGGGACA
1443762 AATATTCAGT
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
37 1 0.02
38 31 0.63
39 4 0.08
40 12 0.24
41 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (38 bp):
ATCAGTGGTCATTCGGGACATCAGTGGTCTTTCGAAAC
Found at i:1443733 original size:20 final size:19
Alignment explanation
Indices: 1443666--1443756 Score: 89
Period size: 20 Copynumber: 4.8 Consensus size: 19
1443656 TCGAGGGATT
* *
1443666 ATCAGTGGTCCTTCGGGAC
1 ATCAGTGGTCATTCGGAAC
*
1443685 AT-AGTGGTTC-TTCGAAAC
1 ATCAGTGG-TCATTCGGAAC
1443703 AATCAGTGGTCATTCGGAAC
1 -ATCAGTGGTCATTCGGAAC
* *
1443723 AATCAGTGGTCTTTCGGGAC
1 -ATCAGTGGTCATTCGGAAC
1443743 AT-AGTGGTCATTCG
1 ATCAGTGGTCATTCG
1443757 AGACAAATAT
Statistics
Matches: 62, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
18 22 0.35
19 10 0.16
20 30 0.48
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (19 bp):
ATCAGTGGTCATTCGGAAC
Found at i:1449652 original size:64 final size:63
Alignment explanation
Indices: 1449584--1449719 Score: 150
Period size: 63 Copynumber: 2.1 Consensus size: 63
1449574 TTTAATGTGC
* * * *
1449584 ATCGATGCACATG-AAGTGTATCGATGCACTTCTTTAAAATAAAAACATCAAATGT-AATTAGTG
1 ATCGATGCACAAGTAA-TGCATCGATGCAC-CCCTTAAAATAAAAACATCAAATGTGAATTA-TG
1449647 T
63 T
* * * *
1449648 ATCGATGCACAAGTAATGCGTCGATGCACCCCTTAAAATACAAACATCGAATGTGATTTATGT
1 ATCGATGCACAAGTAATGCATCGATGCACCCCTTAAAATAAAAACATCAAATGTGAATTATGT
*
1449711 ACCGATGCA
1 ATCGATGCA
1449720 TAGATTGTGC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
63 32 0.52
64 27 0.44
65 2 0.03
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (63 bp):
ATCGATGCACAAGTAATGCATCGATGCACCCCTTAAAATAAAAACATCAAATGTGAATTATGT
Found at i:1450336 original size:18 final size:18
Alignment explanation
Indices: 1450313--1450385 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
1450303 AGGGATTACC
1450313 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
1450331 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
1450350 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
*
1450369 AGTGGTCATTCGGGACA
1 AGTGGTCCTTCGGGACA
1450386 AATATTCAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 30 0.62
19 4 0.08
20 14 0.29
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1451166 original size:14 final size:14
Alignment explanation
Indices: 1451147--1451195 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
1451137 GATATTATTG
1451147 TTATGTGTTCATTA
1 TTATGTGTTCATTA
* *
1451161 TTATGT-CTCACTAA
1 TTATGTGTTCA-TTA
1451175 GTTATGTGTTCATTA
1 -TTATGTGTTCATTA
1451190 TTATGT
1 TTATGT
1451196 CTCACTAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
13 3 0.11
14 14 0.50
15 8 0.29
16 3 0.11
ACGTcount: A:0.22, C:0.10, G:0.14, T:0.53
Consensus pattern (14 bp):
TTATGTGTTCATTA
Found at i:1451179 original size:29 final size:29
Alignment explanation
Indices: 1451146--1451210 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
1451136 TGATATTATT
1451146 GTTATGTGTTCATTATTATGTCTCACTAA
1 GTTATGTGTTCATTATTATGTCTCACTAA
1451175 GTTATGTGTTCATTATTATGTCTCACTAA
1 GTTATGTGTTCATTATTATGTCTCACTAA
1451204 GTCTATG
1 GT-TATG
1451211 ACTTAGCGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 31 0.89
30 4 0.11
ACGTcount: A:0.23, C:0.14, G:0.15, T:0.48
Consensus pattern (29 bp):
GTTATGTGTTCATTATTATGTCTCACTAA
Found at i:1451509 original size:21 final size:22
Alignment explanation
Indices: 1451483--1451534 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
1451473 GAACAAAAGT
*
1451483 ACTGTAGCAGGGTATCAATA-C
1 ACTGTAGCAGGGCATCAATACC
*
1451504 ACTGTAGCAGGGCATCGATACC
1 ACTGTAGCAGGGCATCAATACC
*
1451526 CCTGTAGCA
1 ACTGTAGCA
1451535 TTCTGAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.21
Consensus pattern (22 bp):
ACTGTAGCAGGGCATCAATACC
Found at i:1463474 original size:18 final size:18
Alignment explanation
Indices: 1463451--1463500 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 18
1463441 TATGCCCAAT
1463451 TAGATATATAAACTCAAC
1 TAGATATATAAACTCAAC
* * *
1463469 TAGATAT-T--GCCCAAT
1 TAGATATATAAACTCAAC
1463484 TAGATATATAAACTCAA
1 TAGATATATAAACTCAA
1463501 TTATATATCT
Statistics
Matches: 24, Mismatches: 5, Indels: 6
0.69 0.14 0.17
Matches are distributed among these distances:
15 11 0.46
16 1 0.04
17 1 0.04
18 11 0.46
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.30
Consensus pattern (18 bp):
TAGATATATAAACTCAAC
Found at i:1463503 original size:18 final size:18
Alignment explanation
Indices: 1463447--1463508 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
1463437 CTTTTATGCC
1463447 CAATTAGATATATAAACT
1 CAATTAGATATATAAACT
* * *
1463465 CAACTAGATAT-T--GCC
1 CAATTAGATATATAAACT
1463480 CAATTAGATATATAAACT
1 CAATTAGATATATAAACT
*
1463498 CAATTATATAT
1 CAATTAGATAT
1463509 CTTGGGTTGT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
15 11 0.32
16 1 0.03
17 1 0.03
18 21 0.62
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.34
Consensus pattern (18 bp):
CAATTAGATATATAAACT
Found at i:1474425 original size:37 final size:37
Alignment explanation
Indices: 1474378--1474466 Score: 151
Period size: 37 Copynumber: 2.4 Consensus size: 37
1474368 TTTAGATGTT
*
1474378 TTTTTATTGATAATTTGATTTAATCTTTAATATAATG
1 TTTTTATTGATAATTTGATTTAATCTTTAATATAATA
* *
1474415 TTTTTATTGATAATTTGATTTAATCTTTAATCTAGTA
1 TTTTTATTGATAATTTGATTTAATCTTTAATATAATA
1474452 TTTTTATTGATAATT
1 TTTTTATTGATAATT
1474467 GCTTCATGTG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.30, C:0.03, G:0.08, T:0.58
Consensus pattern (37 bp):
TTTTTATTGATAATTTGATTTAATCTTTAATATAATA
Found at i:1474825 original size:24 final size:23
Alignment explanation
Indices: 1474798--1474843 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
1474788 TAAGTTGCGT
*
1474798 ATATTAAATTTTAATAATAAAAAA
1 ATATTAAATATTAA-AATAAAAAA
* *
1474822 ATATTTAATATTAAATTAAAAA
1 ATATTAAATATTAAAATAAAAA
1474844 TTGAATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
ATATTAAATATTAAAATAAAAAA
Found at i:1474830 original size:18 final size:17
Alignment explanation
Indices: 1474803--1474836 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1474793 TGCGTATATT
1474803 AAATTTTAATAATAAAA
1 AAATTTTAATAATAAAA
*
1474820 AAATATTTAATATTAAA
1 AAAT-TTTAATAATAAA
1474837 TTAAAAATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATTTTAATAATAAAA
Found at i:1486298 original size:21 final size:20
Alignment explanation
Indices: 1486274--1486322 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
1486264 ATGTGTTTTC
1486274 TTTTTAAATATATATAATATT
1 TTTTTAAATATATATAAT-TT
* *
1486295 TTTTTAACTTTATATAATTT
1 TTTTTAAATATATATAATTT
1486315 TTTTTAAA
1 TTTTTAAA
1486323 AAAATTATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTTAAATATATATAATTT
Found at i:1488687 original size:20 final size:20
Alignment explanation
Indices: 1488598--1488869 Score: 210
Period size: 20 Copynumber: 13.5 Consensus size: 20
1488588 GATTTTCCAT
**
1488598 AATCGCAACGCGAA-CATATA
1 AATCGCAACGCGAATC-CGTA
*
1488618 AATCGCAACGCG-ATTC-TA
1 AATCGCAACGCGAATCCGTA
* *
1488636 ACTATCGCAACGAGTATCCGTAA
1 A--ATCGCAACGCGAATCCGT-A
*
1488659 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
1488679 AATCACAACGAC-AATACGTAA
1 AATCGCAACG-CGAATCCGT-A
* * *
1488700 AATCGCAATGTGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
1488720 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
1488740 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGAATCCGTA
* * *
1488760 AATCGCAATGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* * *
1488780 AATCGCAATGCGTATCCATA
1 AATCGCAACGCGAATCCGTA
** *
1488800 AATCGCAATACGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
1488820 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
1488840 AATCGCAATGCGAATCTGTA
1 AATCGCAACGCGAATCCGTA
1488860 AATCGCAACG
1 AATCGCAACG
1488870 AGATTCTGAC
Statistics
Matches: 205, Mismatches: 38, Indels: 18
0.79 0.15 0.07
Matches are distributed among these distances:
18 3 0.01
19 1 0.00
20 163 0.80
21 35 0.17
22 1 0.00
23 2 0.01
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGTA
Found at i:1488755 original size:40 final size:40
Alignment explanation
Indices: 1488598--1488869 Score: 273
Period size: 40 Copynumber: 6.8 Consensus size: 40
1488588 GATTTTCCAT
* * ** *
1488598 AATCGCAACGCGAACATATAAATCGCAACGCG-ATTC-TA
1 AATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTA
* *
1488636 ACTATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTA
1 A--ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCCGTA
* * * *
1488679 AATCACAACGACAATACGTAAAATCGCAATGTGTATCCGTA
1 AATCGCAACGAGAATACGT-AAATCGCAACGCGTATCCGTA
*
1488720 AATCGCAACGAGAATACGTAAATCGCAACGCGTATCTGTA
1 AATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTA
* * *
1488760 AATCGCAATGAGAATACGTAAATCGCAATGCGTATCCATA
1 AATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTA
* * * *
1488800 AATCGCAA-TACGAATACGTAAATCGCAATGCGAATACGTA
1 AATCGCAACGA-GAATACGTAAATCGCAACGCGTATCCGTA
* *
1488840 AATCGCAATGCGAAT-CTGTAAATCGCAACG
1 AATCGCAACGAGAATAC-GTAAATCGCAACG
1488870 AGATTCTGAC
Statistics
Matches: 197, Mismatches: 29, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
38 1 0.01
39 2 0.01
40 124 0.63
41 64 0.32
42 3 0.02
43 3 0.02
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.21
Consensus pattern (40 bp):
AATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTA
Found at i:1488802 original size:60 final size:60
Alignment explanation
Indices: 1488598--1488869 Score: 248
Period size: 60 Copynumber: 4.5 Consensus size: 60
1488588 GATTTTCCAT
** * * * *
1488598 AATCGCAACGCGAA-CATATAAATCGCAACGCG-ATTC-TAACTATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATC-CGTAAATCGCAACGCGAATACGTAA--ATCGCAATGAGAATACGT-A
* * * * *
1488659 AATCGCAACGCGTATCCGTAAATCACAACGAC-AATACGTAAAATCGCAATGTGTATCCGTA
1 AATCGCAACGCGAATCCGTAAATCGCAACG-CGAATACGT-AAATCGCAATGAGAATACGTA
* * *
1488720 AATCGCAACGAGAATACGTAAATCGCAACGCGTAT-CTGTAAATCGCAATGAGAATACGTA
1 AATCGCAACGCGAATCCGTAAATCGCAACGCGAATAC-GTAAATCGCAATGAGAATACGTA
* * * ** *
1488780 AATCGCAATGCGTATCCATAAATCGCAATACGAATACGTAAATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATCCGTAAATCGCAACGCGAATACGTAAATCGCAATGAGAATACGTA
* *
1488840 AATCGCAATGCGAATCTGTAAATCGCAACG
1 AATCGCAACGCGAATCCGTAAATCGCAACG
1488870 AGATTCTGAC
Statistics
Matches: 174, Mismatches: 29, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
60 94 0.54
61 56 0.32
62 21 0.12
63 1 0.01
64 2 0.01
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.21
Consensus pattern (60 bp):
AATCGCAACGCGAATCCGTAAATCGCAACGCGAATACGTAAATCGCAATGAGAATACGTA
Found at i:1489756 original size:24 final size:24
Alignment explanation
Indices: 1489729--1489782 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1489719 GTATTCGAAA
1489729 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1489753 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1489777 TTTGAT
1 TTTGAT
1489783 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1492276 original size:33 final size:33
Alignment explanation
Indices: 1492230--1492314 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 33
1492220 TCGCAACGCG
**
1492230 GAAATGACTATCGCAACGAGAGAATCACAATGC
1 GAAATGAAAATCGCAACGAGAGAATCACAATGC
* *
1492263 GAAATGAAAATCGCAACGAGTGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCACAATGC
1492296 GAAAATGAAAATCGCAACG
1 G-AAATGAAAATCGCAACG
1492315 CGAAACTAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 30 0.64
34 17 0.36
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCACAATGC
Found at i:1492349 original size:20 final size:19
Alignment explanation
Indices: 1492323--1492410 Score: 87
Period size: 20 Copynumber: 4.8 Consensus size: 19
1492313 CGCGAAACTA
1492323 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
*
1492342 ATTTTCGCATTGCGA--TTC
1 A-TTTCGCGTTGCGATTTTC
* *
1492360 A---CTCGTTGTGATTTTC
1 ATTTCGCGTTGCGATTTTC
*
1492376 ATTTCGCATTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
1492395 ATTTCCGCGTTGCGAT
1 ATTT-CGCGTTGCGAT
1492411 AGTCTGTTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
14 7 0.13
16 4 0.07
18 4 0.07
19 17 0.31
20 22 0.41
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:1495918 original size:26 final size:25
Alignment explanation
Indices: 1495867--1495920 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
1495857 ATACCAAGTT
* *
1495867 AGATATACCAAAAACTACACTGTAA
1 AGATATACCAAAAACTAAACTATAA
1495892 AGATATACCAAAAACAATAAAC-ATAA
1 AGATATACCAAAAAC--TAAACTATAA
1495918 AGA
1 AGA
1495921 GTAGTAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 15 0.60
26 6 0.24
27 4 0.16
ACGTcount: A:0.59, C:0.17, G:0.07, T:0.17
Consensus pattern (25 bp):
AGATATACCAAAAACTAAACTATAA
Found at i:1496001 original size:20 final size:20
Alignment explanation
Indices: 1495976--1496037 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
1495966 TTTTGGTTGA
1495976 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
1495996 AATGAAAATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
1496015 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
1496035 AAT
1 AAT
1496038 CGCAACGCGA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
19 18 0.46
20 21 0.54
ACGTcount: A:0.50, C:0.16, G:0.23, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:1496020 original size:19 final size:19
Alignment explanation
Indices: 1495974--1496132 Score: 132
Period size: 19 Copynumber: 9.1 Consensus size: 19
1495964 TCTTTTGGTT
*
1495974 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
1495993 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
1496013 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
1496030 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1496046 GAAATTAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
1496063 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
1496079 GAAATTAAAATAGCAA--C
1 GAAATGAAAATCGCAACGC
*
1496096 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1496112 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1496131 GA
1 GA
1496133 TTTTGGTTTC
Statistics
Matches: 110, Mismatches: 14, Indels: 32
0.71 0.09 0.21
Matches are distributed among these distances:
14 27 0.25
15 3 0.03
16 6 0.05
17 6 0.05
18 3 0.03
19 47 0.43
20 18 0.16
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1496040 original size:14 final size:14
Alignment explanation
Indices: 1496021--1496077 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1496011 GCGAAATGAA
1496021 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
1496035 AATCGCAACGCGAAATTAA
1 AATCGCAA--CG--A-GAG
1496054 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1496068 AATCGCAACG
1 AATCGCAACG
1496078 CGAAATTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1496044 original size:33 final size:33
Alignment explanation
Indices: 1495974--1496127 Score: 227
Period size: 33 Copynumber: 4.5 Consensus size: 33
1495964 TCTTTTGGTT
1495974 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAAC--GAG-A-G--AATCGCAACGC
1496013 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
1496046 GAAATTAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1496079 GAAATTAAAATAGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1496112 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1496128 TGCGATTTTG
Statistics
Matches: 111, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
33 89 0.80
35 1 0.01
36 1 0.01
37 3 0.03
39 17 0.15
ACGTcount: A:0.48, C:0.19, G:0.22, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1496247 original size:20 final size:20
Alignment explanation
Indices: 1496159--1496249 Score: 89
Period size: 20 Copynumber: 4.5 Consensus size: 20
1496149 TGATTATCTC
*
1496159 GTTGTGATTTTCATTTTGCA-
1 GTTGCGATTTTCATTTT-CAT
1496179 -TTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
** * *
1496198 CGTTGCGATAGTCAATTTCGT
1 -GTTGCGATTTTCATTTTCAT
1496219 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
1496239 GTTGCGATTTT
1 GTTGCGATTTT
1496250 AAGTTTAGAA
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
19 15 0.26
20 30 0.52
21 13 0.22
ACGTcount: A:0.14, C:0.15, G:0.19, T:0.52
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:1496814 original size:20 final size:20
Alignment explanation
Indices: 1496787--1496959 Score: 175
Period size: 20 Copynumber: 8.6 Consensus size: 20
1496777 CTTTAAAAAT
1496787 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
1496807 CACGTTGCGATTTTACGTATT
1 CGCGTTGCGA-TTTACGGATA
*
1496828 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* ** *
1496848 CGCATTGCGATTTACATATT
1 CGCGTTGCGATTTACGGATA
* * **
1496868 CTCATTGCGATTTATAGATA
1 CGCGTTGCGATTTACGGATA
* *
1496888 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
1496908 CTCGTTGCGATTTACGAATA
1 CGCGTTGCGATTTACGGATA
1496928 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
1496949 CTCGTTGCGAT
1 CGCGTTGCGAT
1496960 AGTCAGAATC
Statistics
Matches: 125, Mismatches: 26, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
20 91 0.73
21 34 0.27
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1496874 original size:40 final size:40
Alignment explanation
Indices: 1496791--1496959 Score: 221
Period size: 40 Copynumber: 4.2 Consensus size: 40
1496781 AAAAATCGCG
* *
1496791 TTGCGATTTACGGATACACGTTGCGATTTTACGTATTCGCA
1 TTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCTCA
* *
1496832 TTGCGATTTACGGATACGCATTGCGATTTACATATTCTCA
1 TTGCGATTTACGGATACGCGTTGCGATTTACGTATTCTCA
** *
1496872 TTGCGATTTATAGATACGCGTTGCGATTTACGTATTCTCG
1 TTGCGATTTACGGATACGCGTTGCGATTTACGTATTCTCA
* * * *
1496912 TTGCGATTTACGAATACGCGTTGCGATTTTACGGATACTCG
1 TTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCTCA
1496953 TTGCGAT
1 TTGCGAT
1496960 AGTCAGAATC
Statistics
Matches: 113, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
40 70 0.62
41 43 0.38
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (40 bp):
TTGCGATTTACGGATACGCGTTGCGATTTACGTATTCTCA
Found at i:1496977 original size:101 final size:101
Alignment explanation
Indices: 1496787--1497000 Score: 254
Period size: 101 Copynumber: 2.1 Consensus size: 101
1496777 CTTTAAAAAT
* *
1496787 CGCGTTGCGATTTACGGATACACGTTGCGATTTTACGTATTCGCATTGCGATTTACGGATACGCA
1 CGCGTTGCGATTTACGGATACACGTTGCGATTTTACGAATACGCATTGCGATTTACGGATACGCA
* * * *
1496852 TTGCGATTTACATATTCTCATTGCGATTTATA-GATA
66 TTGCGATGTACAGAATCGCATTGCGATTTATATG-TA
* * * * *
1496888 CGCGTTGCGATTTACGTATTCTCGTTGCGA-TTTACGAATACGCGTTGCGATTTTACGGATACTC
1 CGCGTTGCGATTTACGGATACACGTTGCGATTTTACGAATACGCATTGCGA-TTTACGGATACGC
* * *
1496952 GTTGCGATAGT-CAGAATCGCGTTGCGATTTATATGTT
65 ATTGCGAT-GTACAGAATCGCATTGCGATTTATATGTA
1496989 CGCGTTGCGATT
1 CGCGTTGCGATT
1497001 ATGGAAAATC
Statistics
Matches: 96, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
100 17 0.18
101 77 0.80
102 2 0.02
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (101 bp):
CGCGTTGCGATTTACGGATACACGTTGCGATTTTACGAATACGCATTGCGATTTACGGATACGCA
TTGCGATGTACAGAATCGCATTGCGATTTATATGTA
Found at i:1497836 original size:2 final size:2
Alignment explanation
Indices: 1497829--1497853 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1497819 AATATTTTAA
1497829 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1497854 GTTTTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1497857 original size:44 final size:44
Alignment explanation
Indices: 1497797--1497891 Score: 151
Period size: 44 Copynumber: 2.2 Consensus size: 44
1497787 TGAAAACGTG
*
1497797 TATATA-ATATATAGTTTTTGAAAATATTTT-AAATATATATATA
1 TATATATATATATAGTTTTTAAAAATATTTTGAAA-ATATATATA
1497840 TATATATATATATAGTTTTTAAAAATATTTTGAAAATATATATA
1 TATATATATATATAGTTTTTAAAAATATTTTGAAAATATATATA
1497884 -ATATATAT
1 TATATATAT
1497892 TTTTTAAAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
43 14 0.29
44 32 0.65
45 3 0.06
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.48
Consensus pattern (44 bp):
TATATATATATATAGTTTTTAAAAATATTTTGAAAATATATATA
Found at i:1497873 original size:83 final size:80
Alignment explanation
Indices: 1497758--1497927 Score: 213
Period size: 81 Copynumber: 2.1 Consensus size: 80
1497748 CTTCGAAAAA
* *
1497758 ATATATAT-TATATATATTTGAAAACATTTTGAAAACGTGTATATAATATATAGTTTTTGAAAAT
1 ATATATATATATATATATTTAAAAACATTTTGAAAA--TATATATAATATATA-TTTTTGAAAAT
1497822 A-TTTT-AAATATATATAT
63 ATTTTTGAAA-ATATATAT
* * *
1497839 ATATATATATATATAGTTTTTAAAAATATTTTGAAAATATATATAATATATATTTTTTAAAATAT
1 ATATATATATATATA-TATTTAAAAACATTTTGAAAATATATATAATATATATTTTTGAAAATAT
*
1497904 TTTTGAAAATGTATAT
65 TTTTGAAAATATATAT
1497920 A-ATATATA
1 ATATATATA
1497928 GTTTTGAATA
Statistics
Matches: 79, Mismatches: 6, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
80 18 0.23
81 34 0.43
82 9 0.11
83 18 0.23
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.47
Consensus pattern (80 bp):
ATATATATATATATATATTTAAAAACATTTTGAAAATATATATAATATATATTTTTGAAAATATT
TTTGAAAATATATAT
Found at i:1497938 original size:35 final size:35
Alignment explanation
Indices: 1497837--1498047 Score: 194
Period size: 37 Copynumber: 5.8 Consensus size: 35
1497827 AAATATATAT
*
1497837 ATATATATATATATATAGTTTTTAAAAATATTTTGAAA
1 ATATATATA-ATATATAG-TTTTGAAAAT-TTTTGAAA
* *
1497875 ATATATATAATATATATTTTTTAAAATATTTTTGAAA
1 ATATATATAATATATA-GTTTTGAAA-ATTTTTGAAA
* *
1497912 ATGTATATAATATATAGTTTTGAATATATTTTTCAAA
1 ATATATATAATATATAGTTTTGAA-A-ATTTTTGAAA
* *
1497949 ATATATAT--TATATAGTTTTGAAAATATATGAAA
1 ATATATATAATATATAGTTTTGAAAATTTTTGAAA
* * * *
1497982 AAATATATATTATATGGTTTTGAAAACAATTTTTAAAA
1 ATATATATAATATATAGTTTTG--AA-AATTTTTGAAA
1498020 ATATATATATATCATATAG-TTTGAAAAT
1 ATATATATA-AT-ATATAGTTTTGAAAAT
1498048 AATTTTTAAT
Statistics
Matches: 146, Mismatches: 17, Indels: 22
0.79 0.09 0.12
Matches are distributed among these distances:
33 14 0.10
34 1 0.01
35 25 0.17
36 9 0.06
37 60 0.41
38 27 0.18
39 5 0.03
40 5 0.03
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.46
Consensus pattern (35 bp):
ATATATATAATATATAGTTTTGAAAATTTTTGAAA
Found at i:1499305 original size:48 final size:47
Alignment explanation
Indices: 1499181--1499316 Score: 136
Period size: 48 Copynumber: 2.9 Consensus size: 47
1499171 TTTTTACTTA
* * *
1499181 CTTTCAAAATTT-AATATTTCTT-TTATTTATTTATTTATTTATTTTTCT
1 CTTTTAAAATTTAAAT-TTTCTTCTT-TTTA-TTATTTCTTTATTTATCT
* *
1499229 -TTTTAAAATTTAACATTTTCACTCTTTTTATTATTTCTTTCTTTATCT
1 CTTTTAAAATTTAA-ATTTTC-TTCTTTTTATTATTTCTTTATTTATCT
*
1499277 CTTTTAAAATTTAAATTTTCTTCATTTTT-TTCTTTCTTTA
1 CTTTTAAAATTTAAATTTTCTTC-TTTTTATTATTTCTTTA
1499317 AACTTGATTA
Statistics
Matches: 74, Mismatches: 8, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
47 21 0.28
48 31 0.42
49 20 0.27
50 2 0.03
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (47 bp):
CTTTTAAAATTTAAATTTTCTTCTTTTTATTATTTCTTTATTTATCT
Found at i:1504027 original size:43 final size:44
Alignment explanation
Indices: 1503980--1504327 Score: 157
Period size: 43 Copynumber: 7.8 Consensus size: 44
1503970 TCAATCTTTT
*
1503980 TTTTTAAATTTTATAATTAAGG-CTCTT-AATTTTTT-AATCATAC
1 TTTTT-AACTTTATAATTAAGGTC-CTTAAATTTTTTCAATCATAC
*
1504023 TTTTTAACTTTATAATTGAGGTCCTTAAATTTTTTCAATCTCACTTTCTACC
1 TTTTTAACTTTATAATTAAGGTCCTTAAATTTTTTCAA--TCA-----TA-C
* * *
1504075 TTTTCTACCTTTATAATTGAA-G-CCCTAAATTTTTT-AATCCTAC
1 TTTT-TAACTTTATAATT-AAGGTCCTTAAATTTTTTCAATCATAC
* *
1504118 TTTTTAACTTTATAATTGAGG-CTCTTAAGTTTTTTCAATC-TCAC
1 TTTTTAACTTTATAATTAAGGTC-CTTAAATTTTTTCAATCAT-AC
* * ** * * * * * *
1504162 TTTATATCTTTGCATTTGAGGACCCT-AATTTTTTTAAT-ATAAT
1 TTTTTAACTTTATAATTAAGGTCCTTAAATTTTTTCAATCAT-AC
* * *
1504205 TTTTTAACTTTATAATTAA-GACTTTAAGTTTTTTCAATC-TCAC
1 TTTTTAACTTTATAATTAAGGTCCTTAAATTTTTTCAATCAT-AC
* * * * *
1504248 TTTCTATCTTTATAATTGAGG-CCCTAAGTTTTTTCAATC-TCAC
1 TTTTTAACTTTATAATTAAGGTCCTTAAATTTTTTCAATCAT-AC
* * * * * * *
1504291 TTTCTACCCTTATAATTGAGGCCCATAAGTTTTTTCA
1 TTTTTAACTTTATAATTAAGGTCCTTAAATTTTTTCA
1504328 TTCTCAATTA
Statistics
Matches: 242, Mismatches: 40, Indels: 45
0.74 0.12 0.14
Matches are distributed among these distances:
41 1 0.00
42 35 0.14
43 122 0.50
44 43 0.18
45 1 0.00
46 3 0.01
49 2 0.01
51 4 0.02
52 17 0.07
53 13 0.05
54 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.49
Consensus pattern (44 bp):
TTTTTAACTTTATAATTAAGGTCCTTAAATTTTTTCAATCATAC
Found at i:1504107 original size:95 final size:91
Alignment explanation
Indices: 1503989--1504333 Score: 313
Period size: 95 Copynumber: 3.8 Consensus size: 91
1503979 TTTTTTAAAT
* * *
1503989 TTTATAATT-AAGGCTCTTAATTTTTTAATCATACTTTTTAACTTTATAATTGAGGTCCTTAAAT
1 TTTATAATTGAA-GCCCTAAATTTTTTAATCATACTTTTTAACTTTATAATTGAGG-CCTTAAGT
* *
1504053 TTTTTCAATCTCACTTTCTACCTTTTCTA
64 TTTTTCAATCTCACTTTCTATCTTTGC-A
*
1504082 CCTTTATAATTGAAGCCCTAAATTTTTTAATCCTACTTTTTAACTTTATAATTGAGGCTCTTAAG
1 --TTTATAATTGAAGCCCTAAATTTTTTAATCATACTTTTTAACTTTATAATTGAGGC-CTTAAG
*
1504147 TTTTTTCAATCTCACTTTATATCTTTGCA
63 TTTTTTCAATCTCACTTTCTATCTTTGCA
* * * * * * *
1504176 -TT-TGA--GGA-CCCTAATTTTTTTAAT-ATAATTTTTTAACTTTATAATTAAGACTTTAAGTT
1 TTTATAATTGAAGCCCTAAATTTTTTAATCAT-ACTTTTTAACTTTATAATTGAGGCCTTAAGTT
1504235 TTTTCAATCTCACTTTCTA----T-C-
65 TTTTCAATCTCACTTTCTATCTTTGCA
* * * * * *
1504256 TTTATAATTGAGGCCCTAAGTTTTTTCAATC-TCACTTTCTACCCTTATAATTGAGGCCCATAAG
1 TTTATAATTGAAGCCCTAAATTTTTT-AATCAT-ACTTTTTAACTTTATAATTGAGG-CCTTAAG
*
1504320 TTTTTTCATTCTCA
63 TTTTTTCAATCTCA
1504334 ATTATTGAGT
Statistics
Matches: 209, Mismatches: 30, Indels: 30
0.78 0.11 0.11
Matches are distributed among these distances:
81 3 0.01
82 3 0.01
84 1 0.00
85 12 0.06
86 47 0.22
87 54 0.26
88 2 0.01
90 2 0.01
91 2 0.01
94 2 0.01
95 79 0.38
96 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.49
Consensus pattern (91 bp):
TTTATAATTGAAGCCCTAAATTTTTTAATCATACTTTTTAACTTTATAATTGAGGCCTTAAGTTT
TTTCAATCTCACTTTCTATCTTTGCA
Found at i:1504197 original size:87 final size:86
Alignment explanation
Indices: 1504083--1504333 Score: 290
Period size: 86 Copynumber: 2.9 Consensus size: 86
1504073 CCTTTTCTAC
* * *
1504083 CTTTATAATTGAAGCCCTAAATTTTTTAATCCT-ACTTTTTAACTTTATAATTGAGGCTCTTAAG
1 CTTTACAATTGAGGCCCTAATTTTTTTAAT-CTAACTTTTTAACTTTATAATTGAGGCTCTTAAG
1504147 TTTTTTCAATCTCACTTTATAT
65 TTTTTTCAATCTCACTTTATAT
* * * * * *
1504169 CTTTGCATTTGAGGACCCTAATTTTTTTAATATAATTTTTTAACTTTATAATTAAGACT-TTAAG
1 CTTTACAATTGAGG-CCCTAATTTTTTTAATCTAACTTTTTAACTTTATAATTGAGGCTCTTAAG
*
1504233 TTTTTTCAATCTCACTTTCTAT
65 TTTTTTCAATCTCACTTTATAT
* * * * * * * *
1504255 CTTTATAATTGAGGCCCTAAGTTTTTTCAATCTCACTTTCTACCCTTATAATTGAGGCCCATAAG
1 CTTTACAATTGAGGCCCTAA-TTTTTTTAATCTAACTTTTTAACTTTATAATTGAGGCTCTTAAG
*
1504320 TTTTTTCATTCTCA
65 TTTTTTCAATCTCA
1504334 ATTATTGAGT
Statistics
Matches: 136, Mismatches: 25, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
85 6 0.04
86 76 0.56
87 54 0.40
ACGTcount: A:0.27, C:0.18, G:0.08, T:0.48
Consensus pattern (86 bp):
CTTTACAATTGAGGCCCTAATTTTTTTAATCTAACTTTTTAACTTTATAATTGAGGCTCTTAAGT
TTTTTCAATCTCACTTTATAT
Found at i:1505471 original size:14 final size:14
Alignment explanation
Indices: 1505452--1505496 Score: 72
Period size: 14 Copynumber: 3.1 Consensus size: 14
1505442 CCCTCTGTTT
1505452 GAACATAAATGAAC
1 GAACATAAATGAAC
1505466 GAACATAAATGAAC
1 GAACATAAATGAAC
1505480 GAACATATAATCGAAC
1 GAACATA-AAT-GAAC
1505496 G
1 G
1505497 TTCACGAACG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
14 21 0.72
15 3 0.10
16 5 0.17
ACGTcount: A:0.53, C:0.16, G:0.16, T:0.16
Consensus pattern (14 bp):
GAACATAAATGAAC
Found at i:1505768 original size:42 final size:42
Alignment explanation
Indices: 1505707--1505790 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
1505697 AACCGGATAC
* * *
1505707 TAATATATTTATTTATTTAAATAGATTACTACTGCCACTCTT
1 TAATATATTTATTTATTTAAATAAATCACTACTACCACTCTT
*
1505749 TAATTTATTTATTTATTTAAATAAATCACTACTACCACTCTT
1 TAATATATTTATTTATTTAAATAAATCACTACTACCACTCTT
1505791 ATCTTTGAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.35, C:0.15, G:0.02, T:0.48
Consensus pattern (42 bp):
TAATATATTTATTTATTTAAATAAATCACTACTACCACTCTT
Found at i:1506827 original size:16 final size:16
Alignment explanation
Indices: 1506808--1506841 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1506798 CAATATACGA
1506808 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
1506824 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
1506840 AT
1 AT
1506842 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:1506915 original size:16 final size:18
Alignment explanation
Indices: 1506883--1506916 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1506873 TATTAATGTA
1506883 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
1506901 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
1506917 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:1513589 original size:48 final size:48
Alignment explanation
Indices: 1513528--1513643 Score: 146
Period size: 48 Copynumber: 2.4 Consensus size: 48
1513518 TCTTTTAGGA
* * * * *
1513528 TTAGATTTATTATT-TTATTAGGAATTAAGATATAGT-TAAAATATTATCT
1 TTAG-TTTATTATTATT-TTAAGAATTAAGATAGAATCT-AAACATTATAT
1513577 TTAGTTTATTATTATTTTAAGAATTAAGATAGAATCTAAACATTATAT
1 TTAGTTTATTATTATTTTAAGAATTAAGATAGAATCTAAACATTATAT
1513625 TTAGTTTATTATTATTTTA
1 TTAGTTTATTATTATTTTA
1513644 TTCAGTAGTT
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
48 53 0.88
49 7 0.12
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.51
Consensus pattern (48 bp):
TTAGTTTATTATTATTTTAAGAATTAAGATAGAATCTAAACATTATAT
Found at i:1515484 original size:22 final size:22
Alignment explanation
Indices: 1515456--1515508 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
1515446 TGTAAAGGTG
1515456 TATCGATACCTGTTGAGAGTGA
1 TATCGATACCTGTTGAGAGTGA
*
1515478 TATCGATACCTGTTGAGAGTGG
1 TATCGATACCTGTTGAGAGTGA
1515500 TATCGATAC
1 TATCGATAC
1515509 TTTAAGGGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.32
Consensus pattern (22 bp):
TATCGATACCTGTTGAGAGTGA
Found at i:1515554 original size:21 final size:21
Alignment explanation
Indices: 1515497--1515556 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 21
1515487 CTGTTGAGAG
*
1515497 TGGTATCGATACTTTAAGGGA
1 TGGTATCGATACCTTAAGGGA
1515518 TAGGTATC-AGTACCTTAA-GGA
1 T-GGTATCGA-TACCTTAAGGGA
1515539 TGGTATCGATACCCTTAA
1 TGGTATCGATA-CCTTAA
1515557 AACATCGAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
20 8 0.24
21 13 0.38
22 13 0.38
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (21 bp):
TGGTATCGATACCTTAAGGGA
Found at i:1515631 original size:54 final size:54
Alignment explanation
Indices: 1515520--1515664 Score: 159
Period size: 54 Copynumber: 2.7 Consensus size: 54
1515510 TTAAGGGATA
* * * **
1515520 GGTATCAGTACCTTAAGGATGGTATCGATACCCTTAAAACATCGAATGTTAGATT
1 GGTATCGGTACCTTGAGGA-GGTATCGATACCCTTGAAACATCGAACCTTAGATT
* * **
1515575 GGTATTGGTACCTTGAGGAGGTATTGATACCCTTGAAACATCGAACCTTATTTT
1 GGTATCGGTACCTTGAGGAGGTATCGATACCCTTGAAACATCGAACCTTAGATT
* *
1515629 GGTATCGGTA-CATGCA-GAGGTATCGATACACTTGAA
1 GGTATCGGTACCTTG-AGGAGGTATCGATACCCTTGAA
1515665 GGGTGGTATC
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
53 21 0.28
54 39 0.51
55 16 0.21
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.31
Consensus pattern (54 bp):
GGTATCGGTACCTTGAGGAGGTATCGATACCCTTGAAACATCGAACCTTAGATT
Found at i:1515675 original size:22 final size:20
Alignment explanation
Indices: 1515647--1515697 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 20
1515637 TACATGCAGA
1515647 GGTATCGATACACTTGAAGGGT
1 GGTATCGATACACTT--AGGGT
* *
1515669 GGTATCGGTACCCTTAGGGT
1 GGTATCGATACACTTAGGGT
*
1515689 GGTACCGAT
1 GGTATCGAT
1515698 GCCTCTAAGC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 12 0.48
22 13 0.52
ACGTcount: A:0.22, C:0.18, G:0.33, T:0.27
Consensus pattern (20 bp):
GGTATCGATACACTTAGGGT
Found at i:1517646 original size:25 final size:25
Alignment explanation
Indices: 1517611--1517658 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
1517601 ATCATGATTA
1517611 TCCTATATGGGAACAAGTACATTTG
1 TCCTATATGGGAACAAGTACATTTG
*
1517636 TCCTATGTGGGAACAAGTACATT
1 TCCTATATGGGAACAAGTACATT
1517659 AAATAACGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (25 bp):
TCCTATATGGGAACAAGTACATTTG
Found at i:1519702 original size:15 final size:15
Alignment explanation
Indices: 1519682--1519719 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1519672 GAGAGATGAA
1519682 ATTTTTTAGAGAAAT
1 ATTTTTTAGAGAAAT
*
1519697 ATTTTTTAAGAGACAT
1 ATTTTTT-AGAGAAAT
1519713 -TTTTTTA
1 ATTTTTTA
1519720 CAAAAACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 13 0.62
16 7 0.33
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (15 bp):
ATTTTTTAGAGAAAT
Found at i:1519734 original size:30 final size:32
Alignment explanation
Indices: 1519700--1519760 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
1519690 GAGAAATATT
*
1519700 TTTTAA-GAGACA-TTTTTTTACAAAAACAAA
1 TTTTAAGGAAACATTTTTTTTACAAAAACAAA
*
1519730 TTTTAAGGGAAATATTTTTTTTACAAAAACA
1 TTTTAA-GGAAACATTTTTTTTACAAAAACA
1519761 TGTTTTGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 6 0.23
32 4 0.15
33 16 0.62
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.39
Consensus pattern (32 bp):
TTTTAAGGAAACATTTTTTTTACAAAAACAAA
Found at i:1519940 original size:37 final size:37
Alignment explanation
Indices: 1519864--1520071 Score: 257
Period size: 37 Copynumber: 5.8 Consensus size: 37
1519854 TTATTTTGAG
*
1519864 AGAAAAA-AATCTCAAGTGAGAT--GATTT-TTTTTA
1 AGAAAAACAATCTCAAGTGAGATAAAATTTGTTTTTA
* *
1519897 AGAAAAACAATCTCAAATGAGACAAAATTTGTTTTTA
1 AGAAAAACAATCTCAAGTGAGATAAAATTTGTTTTTA
**
1519934 AGAAAAACAATCT-AGAGTGAGACGAAATTTGTTTTTA
1 AGAAAAACAATCTCA-AGTGAGATAAAATTTGTTTTTA
** *
1519971 AG-AATGCAATCTCAAGTGAGATGAAATTTGTTTTTA
1 AGAAAAACAATCTCAAGTGAGATAAAATTTGTTTTTA
* *
1520007 AGAAAAACAATCTTAAGTGAGATAAGATTTGTTTTTA
1 AGAAAAACAATCTCAAGTGAGATAAAATTTGTTTTTA
* *
1520044 AAAAAAACACTCTCAAGTGAGATAAAAT
1 AGAAAAACAATCTCAAGTGAGATAAAAT
1520072 CTTATGTGAA
Statistics
Matches: 151, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
33 7 0.05
34 13 0.09
36 36 0.24
37 95 0.63
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.31
Consensus pattern (37 bp):
AGAAAAACAATCTCAAGTGAGATAAAATTTGTTTTTA
Found at i:1519991 original size:73 final size:71
Alignment explanation
Indices: 1519864--1520071 Score: 244
Period size: 73 Copynumber: 2.9 Consensus size: 71
1519854 TTATTTTGAG
* *
1519864 AGAAAAA-AATCTCAAGTGAGATG--ATTT-TTTTTAAGAAAAACAATCTCAAATGAGACAAAAT
1 AGAAAAACAATCT-AAGTGAGA-GAAATTTGTTTTTAAG-AAAACAATCTCAAGTGAGATAAAAT
1519925 TTGTTTTTA
63 TTGTTTTTA
** *
1519934 AGAAAAACAATCTAGAGTGAGACGAAATTTGTTTTTAAGAATGCAATCTCAAGTGAGATGAAATT
1 AGAAAAACAATCTA-AGTGAGA-GAAATTTGTTTTTAAGAAAACAATCTCAAGTGAGATAAAATT
1519999 TGTTTTTA
64 TGTTTTTA
* * *
1520007 AGAAAAACAATCTTAAGTGAGATAAGATTTGTTTTTAAAAAAAACACTCTCAAGTGAGATAAAAT
1 AGAAAAACAATC-TAAGTGAGAGAA-ATTTGTTTTT-AAGAAAACAATCTCAAGTGAGATAAAAT
1520072 CTTATGTGAA
Statistics
Matches: 118, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
70 8 0.07
71 13 0.11
72 2 0.02
73 62 0.53
74 33 0.28
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.31
Consensus pattern (71 bp):
AGAAAAACAATCTAAGTGAGAGAAATTTGTTTTTAAGAAAACAATCTCAAGTGAGATAAAATTTG
TTTTTA
Found at i:1520369 original size:116 final size:115
Alignment explanation
Indices: 1520213--1520499 Score: 274
Period size: 116 Copynumber: 2.5 Consensus size: 115
1520203 ATTGGATAAA
* * * *
1520213 TTCTTCTCGTTATGAACCCTT-TCATTGGATATATTTATCCACATTCTTCTGTAATAGACGAACC
1 TTCTTCTCATTATGAACCCTTCT-ATTGGA-AAAGTGATCCACATTCTTCTGTAATAGACGAACC
* * * * *
1520277 AATGTTAAACAAGTTCTACTCATTAGGAACTTATTTTCCCTT-ATCAGTCGAG
64 AAGGCTAAACAAGTTCTACTCATTAAGAACTTATTCT-CCTTCATCAGACGAG
* * * * * * *
1520329 TTCTTCTCATTATGAACCCTTCTATTGGAAAAGCTGATCCACCTCCTTCTATGATGGATGAGCCA
1 TTCTTCTCATTATGAACCCTTCTATTGGAAAAG-TGATCCACATTCTTCTGTAATAGACGAACCA
* * * * **
1520394 AGGCTGAACAAGTTCTTCTCATTAAGAACTTCTTCTCCTTCATCGGACGTT
65 AGGCTAAACAAGTTCTACTCATTAAGAACTTATTCTCCTTCATCAGACGAG
* * *
1520445 TTCTTCTCATTATGAACCTTTCCATTGGAAATGTCGATCCACATAT-TTCTGTAAT
1 TTCTTCTCATTATGAACCCTTCTATTGGAAAAGT-GATCCACAT-TCTTCTGTAAT
1520500 GGGCGAGAAA
Statistics
Matches: 137, Mismatches: 29, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
115 7 0.05
116 129 0.94
117 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (115 bp):
TTCTTCTCATTATGAACCCTTCTATTGGAAAAGTGATCCACATTCTTCTGTAATAGACGAACCAA
GGCTAAACAAGTTCTACTCATTAAGAACTTATTCTCCTTCATCAGACGAG
Found at i:1520938 original size:24 final size:24
Alignment explanation
Indices: 1520891--1520967 Score: 115
Period size: 24 Copynumber: 3.3 Consensus size: 24
1520881 TAGAATTTTG
*
1520891 ATTAGGA-TTTTA-ATTATT-TATT
1 ATTAGGATTTTTAGTTTATTAT-TT
1520913 ATTAGGATTTTTAGTTTATTATTT
1 ATTAGGATTTTTAGTTTATTATTT
1520937 ATTAGGATTTTTAGTTTATTATTT
1 ATTAGGATTTTTAGTTTATTATTT
1520961 ATTAGGA
1 ATTAGGA
1520968 ATTTAAATGT
Statistics
Matches: 51, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
22 7 0.14
23 5 0.10
24 38 0.75
25 1 0.02
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (24 bp):
ATTAGGATTTTTAGTTTATTATTT
Found at i:1527729 original size:15 final size:15
Alignment explanation
Indices: 1527709--1527737 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1527699 AAAGTGTGAC
1527709 ATGAGCTATGTGATA
1 ATGAGCTATGTGATA
1527724 ATGAGCTATGTGAT
1 ATGAGCTATGTGAT
1527738 TATATGCCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.07, G:0.28, T:0.34
Consensus pattern (15 bp):
ATGAGCTATGTGATA
Found at i:1527756 original size:15 final size:16
Alignment explanation
Indices: 1527709--1527756 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
1527699 AAAGTGTGAC
*
1527709 ATGAGCTATGTGATA-
1 ATGACCTATGTGATAT
*
1527724 ATGAGCTATGTGATTAT
1 ATGACCTATGTGA-TAT
1527741 ATG-CCTATGTGATAT
1 ATGACCTATGTGATAT
1527756 A
1 A
1527757 AGTTATGTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 17 0.57
16 10 0.33
17 3 0.10
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (16 bp):
ATGACCTATGTGATAT
Found at i:1527942 original size:23 final size:23
Alignment explanation
Indices: 1527866--1527944 Score: 88
Period size: 23 Copynumber: 3.4 Consensus size: 23
1527856 TTGGGGATAA
* *
1527866 TTCTATGTAGTCATTCGGGACAT
1 TTCTATGTGGTCCTTCGGGACAT
* * *
1527889 TTCTATGCGATCCTTTGGGACAAT
1 TTCTATGTGGTCCTTCGGGAC-AT
*
1527913 AT-TATGTGGTCCTTCGGGACAT
1 TTCTATGTGGTCCTTCGGGACAT
1527935 TTCTATGTGG
1 TTCTATGTGG
1527945 CAATTTGGTG
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
22 3 0.07
23 38 0.86
24 3 0.07
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (23 bp):
TTCTATGTGGTCCTTCGGGACAT
Found at i:1527963 original size:24 final size:24
Alignment explanation
Indices: 1527933--1527984 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1527923 CCTTCGGGAC
* *
1527933 ATTTCTATGTGGCAATTTGGTGCA
1 ATTTCTATGCGACAATTTGGTGCA
*
1527957 ATTTCTATGCGACACTTTGGTGCA
1 ATTTCTATGCGACAATTTGGTGCA
1527981 ATTT
1 ATTT
1527985 ATACGAGCTG
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:0.21, C:0.15, G:0.21, T:0.42
Consensus pattern (24 bp):
ATTTCTATGCGACAATTTGGTGCA
Found at i:1536029 original size:15 final size:16
Alignment explanation
Indices: 1535994--1536035 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1535984 GCCACTGTGT
*
1535994 GTGTGTTATTTTATCTT
1 GTGTGTTATTTTA-CTA
1536011 GTGTGTTATTTTA-TA
1 GTGTGTTATTTTACTA
*
1536026 GTGTTTTATT
1 GTGTGTTATT
1536036 CTACATTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
17 13 0.57
ACGTcount: A:0.14, C:0.02, G:0.19, T:0.64
Consensus pattern (16 bp):
GTGTGTTATTTTACTA
Found at i:1538580 original size:2 final size:2
Alignment explanation
Indices: 1538573--1538614 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1538563 TTTACTGTGA
1538573 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1538615 TCTATAAAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1545249 original size:24 final size:21
Alignment explanation
Indices: 1545222--1545279 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 21
1545212 ATGTGAAATA
1545222 ATGAAAGTGATCACATGTGTGTAT
1 ATGAAAGTGAT-ACATGT-T-TAT
1545246 ATG-AAGTGAAATACATGTTTAT
1 ATGAAAGTG--ATACATGTTTAT
1545268 ATGAAAAGTGAT
1 ATG-AAAGTGAT
1545280 GAGAAGATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
22 8 0.27
23 6 0.20
24 14 0.47
25 2 0.07
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33
Consensus pattern (21 bp):
ATGAAAGTGATACATGTTTAT
Found at i:1545505 original size:22 final size:20
Alignment explanation
Indices: 1545477--1545554 Score: 106
Period size: 20 Copynumber: 3.9 Consensus size: 20
1545467 GTTCTTAAGG
1545477 AGTGGTCCTTCGGGACATATAC
1 AGTGGTCCTTCGGGACA-AT-C
1545499 AGTGGTCCTTCGGGAC-AT-
1 AGTGGTCCTTCGGGACAATC
* *
1545517 AGTGGTTCTTCGGAACAATC
1 AGTGGTCCTTCGGGACAATC
1545537 AGTGGTCCTTCGGGACAA
1 AGTGGTCCTTCGGGACAA
1545555 ATATTCAGTG
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
18 14 0.28
19 2 0.04
20 18 0.36
22 16 0.32
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (20 bp):
AGTGGTCCTTCGGGACAATC
Found at i:1545547 original size:38 final size:40
Alignment explanation
Indices: 1545477--1545553 Score: 122
Period size: 38 Copynumber: 2.0 Consensus size: 40
1545467 GTTCTTAAGG
*
1545477 AGTGGTCCTTCGGGACATATACAGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGAACATATACAGTGGTCCTTCGGGACAT
*
1545517 AGTGGTTCTTCGGAACA-AT-CAGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGAACATATACAGTGGTCCTTCGGGACA
1545554 AATATTCAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 18 0.51
39 2 0.06
40 15 0.43
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (40 bp):
AGTGGTCCTTCGGAACATATACAGTGGTCCTTCGGGACAT
Found at i:1547340 original size:113 final size:113
Alignment explanation
Indices: 1547142--1547367 Score: 452
Period size: 113 Copynumber: 2.0 Consensus size: 113
1547132 ATATATAAAT
1547142 ACAGCTTCAAGAAACCAAGACACATCTGACCATCATATGACCTGCAATAACATTTGCACAAAAGA
1 ACAGCTTCAAGAAACCAAGACACATCTGACCATCATATGACCTGCAATAACATTTGCACAAAAGA
1547207 AAGTGAAGTTGTTCACATTATTATTTTTAAAAAAAAAATAAGTACGTA
66 AAGTGAAGTTGTTCACATTATTATTTTTAAAAAAAAAATAAGTACGTA
1547255 ACAGCTTCAAGAAACCAAGACACATCTGACCATCATATGACCTGCAATAACATTTGCACAAAAGA
1 ACAGCTTCAAGAAACCAAGACACATCTGACCATCATATGACCTGCAATAACATTTGCACAAAAGA
1547320 AAGTGAAGTTGTTCACATTATTATTTTTAAAAAAAAAATAAGTACGTA
66 AAGTGAAGTTGTTCACATTATTATTTTTAAAAAAAAAATAAGTACGTA
1547368 GATCGCATTA
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 113 1.00
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (113 bp):
ACAGCTTCAAGAAACCAAGACACATCTGACCATCATATGACCTGCAATAACATTTGCACAAAAGA
AAGTGAAGTTGTTCACATTATTATTTTTAAAAAAAAAATAAGTACGTA
Found at i:1549802 original size:17 final size:17
Alignment explanation
Indices: 1549761--1549795 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1549751 TTCAGCGCTT
1549761 GCTCCCTTCCAAAACAA
1 GCTCCCTTCCAAAACAA
1549778 GCTCCCTTCCAAAACAA
1 GCTCCCTTCCAAAACAA
1549795 G
1 G
1549796 GCCCCTTTAA
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:0.40, G:0.09, T:0.17
Consensus pattern (17 bp):
GCTCCCTTCCAAAACAA
Found at i:1550840 original size:12 final size:12
Alignment explanation
Indices: 1550813--1550844 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
1550803 TCATCAAAAA
1550813 ATATTTTTAAAT
1 ATATTTTTAAAT
1550825 -TATTTTTAAAT
1 ATATTTTTAAAT
1550836 ATATTTTTA
1 ATATTTTTA
1550845 TAAGTGTCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
ATATTTTTAAAT
Found at i:1551551 original size:17 final size:18
Alignment explanation
Indices: 1551529--1551562 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1551519 TATGGTTAAA
1551529 TAATAATAA-TAAAATAG
1 TAATAATAATTAAAATAG
1551546 TAATAATAATTAAAATA
1 TAATAATAATTAAAATA
1551563 AACATTAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (18 bp):
TAATAATAATTAAAATAG
Found at i:1552851 original size:3 final size:3
Alignment explanation
Indices: 1552843--1552902 Score: 77
Period size: 3 Copynumber: 19.7 Consensus size: 3
1552833 GGCCTGTTTG
* *
1552843 TAA TAA TAA TAA TAT TAA TAA TAA AAA TATA TAA TAAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA TAA
1552890 T-A TAA TAA TAA TA
1 TAA TAA TAA TAA TA
1552903 TAAATAAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 2 0.04
3 42 0.84
4 6 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1552882 original size:26 final size:28
Alignment explanation
Indices: 1552848--1552905 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 28
1552838 GTTTGTAATA
*
1552848 ATAATAATAT-TAAT-AATAAAAAT-AT
1 ATAATAATATATAATAAATAATAATAAT
1552873 ATAATAA-ATAATAATAATATAATAATAAT
1 ATAATAATAT-ATAATAA-ATAATAATAAT
1552902 ATAA
1 ATAA
1552906 ATAAAATCGG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 2 0.07
25 7 0.26
26 4 0.15
27 1 0.04
28 7 0.26
29 6 0.22
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (28 bp):
ATAATAATATATAATAAATAATAATAAT
Found at i:1552884 original size:20 final size:21
Alignment explanation
Indices: 1552848--1552911 Score: 76
Period size: 20 Copynumber: 2.9 Consensus size: 21
1552838 GTTTGTAATA
1552848 ATAATAATATTAATAATAAAAAT
1 ATAATAATA--AATAATAAAAAT
*
1552871 AT-ATAATAAATAATAATAAT
1 ATAATAATAAATAATAAAAAT
1552891 ATAATAATAATATAAATAAAA
1 ATAATAATAA-AT-AATAAAA
1552912 TCGGGACAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
20 13 0.36
21 7 0.19
22 8 0.22
23 8 0.22
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAATAATAAATAATAAAAAT
Found at i:1552906 original size:26 final size:24
Alignment explanation
Indices: 1552844--1552909 Score: 84
Period size: 23 Copynumber: 2.8 Consensus size: 24
1552834 GCCTGTTTGT
*
1552844 AATAATAATAATATTAATAATAAA
1 AATAATAATAATATAAATAATAAA
1552868 AATATATAATAA-AT-AATAAT-AA
1 AATA-ATAATAATATAAATAATAAA
*
1552890 TATAATAATAATATAAATAA
1 AATAATAATAATATAAATAA
1552910 AATCGGGACA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
21 7 0.18
22 7 0.18
23 11 0.29
24 6 0.16
25 7 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
AATAATAATAATATAAATAATAAA
Found at i:1553608 original size:113 final size:112
Alignment explanation
Indices: 1553410--1554027 Score: 798
Period size: 113 Copynumber: 5.5 Consensus size: 112
1553400 AAGTCGAACA
** *
1553410 AGTTCTTCTCATTATGAACTTCCTCTGGAAATGCTGATCCATCAAGTGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTATCTGGAAATGCTGATCCATCAAGTGATGGATTTAAGCAAAA-
*
1553475 GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
65 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
* *
1553523 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTATCTGGAAATGCTGATCCATCAAGTGATGGATTTAAGCAAAAG
* * *
1553588 TTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATG
66 -TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
* * * * * * *
1553636 AGTTCTTCTCATTATGAACTCTAACTGGCACTGCTGATCCACCGAGTGATGAATTTAAGCAAAAA
1 AGTTCTTCTCATTATGAACTTTATCTGGAAATGCTGATCCATCAAGTGATGGATTTAAGC-AAAA
*
1553701 GTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATG
65 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
* * *
1553749 AGTTCTTCTTATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTATCTGGAAATGCTGATCCATCAAGTGATGGATTTAAGCAAAAG
*
1553814 ATTGAACAAATTCTTCTCATTATGAA-TTCTTC-T--TTCTTC-GATG
66 -TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
* * * * * * *
1553857 AGTTCTTCTCATTATGAACTCTAACTGGCACTGCTGATCCACCGAGTGATGAATTTAAGCAAAAA
1 AGTTCTTCTCATTATGAACTTTATCTGGAAATGCTGATCCATCAAGTGATGGATTTAAGC-AAAA
* * *
1553922 GTTGAACAAGTTCTTCTAATTATGAACTTCTTCTTTCTTCTTAAGATG
65 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
* * * * * * *
1553970 AGTTCTTCTCATTTTGAACTCTAACTGGCACTGTTGATCCATTGAA-TGATGGATTTAA
1 AGTTCTTCTCATTATGAACTTTATCTGGAAATGCTGATCCA-TCAAGTGATGGATTTAA
1554028 ATCTTTGCTA
Statistics
Matches: 443, Mismatches: 52, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
108 77 0.17
109 17 0.04
110 1 0.00
111 1 0.00
112 16 0.04
113 325 0.73
114 6 0.01
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (112 bp):
AGTTCTTCTCATTATGAACTTTATCTGGAAATGCTGATCCATCAAGTGATGGATTTAAGCAAAAG
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
Found at i:1553843 original size:16 final size:16
Alignment explanation
Indices: 1553822--1553874 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 16
1553812 AGATTGAACA
1553822 AATTCTTCTCATTATG
1 AATTCTTCTCATTATG
1553838 AATTCTTCTTTC-TTCGATG
1 AATTCTTC--TCATT--ATG
*
1553857 AGTTCTTCTCATTATG
1 AATTCTTCTCATTATG
1553873 AA
1 AA
1553875 CTCTAACTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
16 12 0.40
17 4 0.13
18 4 0.13
19 10 0.33
ACGTcount: A:0.23, C:0.19, G:0.09, T:0.49
Consensus pattern (16 bp):
AATTCTTCTCATTATG
Found at i:1554027 original size:221 final size:225
Alignment explanation
Indices: 1553410--1553989 Score: 956
Period size: 226 Copynumber: 2.6 Consensus size: 225
1553400 AAGTCGAACA
* * * * * *
1553410 AGTTCTTCTCATTATGAACTTCCT--CTGGAAATGCTGATCCATCAAGTGATGGATTTGAGCAAA
1 AGTTCTTCTCATTATGAAC-T-CTAACTGGCACTGCTGATCCACCGAGTGATGAATTTAAGCAAA
* *
1553473 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
64 AAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
*
1553538 GAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAGCAAAAGTTTGAACAAATTCTT
129 GAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAGCAAAAGATTGAACAAATTCTT
1553603 CTCATTATGAATTTCTTCTTTCTTCTTCAGATG
194 CTCATTATGAATTTCTTC-TTCTTCTTCAGATG
1553636 AGTTCTTCTCATTATGAACTCTAACTGGCACTGCTGATCCACCGAGTGATGAATTTAAGCAAAAA
1 AGTTCTTCTCATTATGAACTCTAACTGGCACTGCTGATCCACCGAGTGATGAATTTAAGCAAAAA
* *
1553701 GTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGA
66 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1553766 ACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAGCAAAAGATTGAACAAATTCTTCT
131 ACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAGCAAAAGATTGAACAAATTCTTCT
1553831 CATTATGAA-TTCTTC-T-TTCTTC-GATG
196 CATTATGAATTTCTTCTTCTTCTTCAGATG
1553857 AGTTCTTCTCATTATGAACTCTAACTGGCACTGCTGATCCACCGAGTGATGAATTTAAGCAAAAA
1 AGTTCTTCTCATTATGAACTCTAACTGGCACTGCTGATCCACCGAGTGATGAATTTAAGCAAAAA
* * * *
1553922 GTTGAACAAGTTCTTCTAATTATGAACTTCTTCTTTCTTCTTAAGATGAGTTCTTCTCATTTTGA
66 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1553987 ACT
131 ACT
1553990 CTAACTGGCA
Statistics
Matches: 335, Mismatches: 17, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
221 131 0.39
222 6 0.02
223 1 0.00
224 2 0.01
225 7 0.02
226 188 0.56
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (225 bp):
AGTTCTTCTCATTATGAACTCTAACTGGCACTGCTGATCCACCGAGTGATGAATTTAAGCAAAAA
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
ACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAGCAAAAGATTGAACAAATTCTTCT
CATTATGAATTTCTTCTTCTTCTTCAGATG
Found at i:1555187 original size:19 final size:17
Alignment explanation
Indices: 1555159--1555207 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
1555149 CAAATAAAAG
*
1555159 AATAAGTTGAATTTTCGAA
1 AATAAATTGAATTTTC--A
*
1555178 AATAAATTGAA-TCTCA
1 AATAAATTGAATTTTCA
1555194 AATAAATTGAATTT
1 AATAAATTGAATTT
1555208 AGAGAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 3 0.12
19 10 0.38
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (17 bp):
AATAAATTGAATTTTCA
Found at i:1555551 original size:10 final size:10
Alignment explanation
Indices: 1555536--1555607 Score: 81
Period size: 10 Copynumber: 6.5 Consensus size: 10
1555526 TCTTGATCCC
1555536 TTTTTTTCTT
1 TTTTTTTCTT
1555546 TTTTTTTCTTCT
1 TTTTTTTC-T-T
1555558 TCTTATTCTCTCTT
1 T-TT-TT-T-TCTT
1555572 TTTTTTTCTT
1 TTTTTTTCTT
1555582 TTTCTTTTCTT
1 TTT-TTTTCTT
1555593 TTTTTTTCTT
1 TTTTTTTCTT
1555603 TTTTT
1 TTTTT
1555608 CTTCAAGCAT
Statistics
Matches: 55, Mismatches: 0, Indels: 14
0.80 0.00 0.20
Matches are distributed among these distances:
10 27 0.49
11 12 0.22
12 4 0.07
13 4 0.07
14 4 0.07
15 2 0.04
16 2 0.04
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:1555571 original size:26 final size:25
Alignment explanation
Indices: 1555542--1555611 Score: 86
Period size: 26 Copynumber: 2.7 Consensus size: 25
1555532 TCCCTTTTTT
1555542 TCTTTTTTTTTCTTCTTCTTATTCTC
1 TCTTTTTTTTTCTTCTTCTT-TTCTC
* *
1555568 TCTTTTTTTTTCTTTTTCTTTTCTT
1 TCTTTTTTTTTCTTCTTCTTTTCTC
* *
1555593 TTTTTTTCTTTTTTTCTTC
1 TCTTTTT-TTTTCTTCTTC
1555612 AAGCATAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
25 10 0.26
26 28 0.74
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.80
Consensus pattern (25 bp):
TCTTTTTTTTTCTTCTTCTTTTCTC
Found at i:1555580 original size:23 final size:21
Alignment explanation
Indices: 1555546--1555602 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
1555536 TTTTTTTCTT
1555546 TTTTTTTCTTCTTCTTATTCTCTC
1 TTTTTTT-TTCTTCTTATT-T-TC
* *
1555570 TTTTTTTTTCTTTTTCTTTTC
1 TTTTTTTTTCTTCTTATTTTC
1555591 TTTTTTTTTCTT
1 TTTTTTTTTCTT
1555603 TTTTTCTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 14 0.45
22 1 0.03
23 9 0.29
24 7 0.23
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTTTTTTTCTTCTTATTTTC
Found at i:1555595 original size:6 final size:6
Alignment explanation
Indices: 1555538--1555605 Score: 58
Period size: 5 Copynumber: 11.8 Consensus size: 6
1555528 TTGATCCCTT
*
1555538 TTTTTC -TTTT- TTTTTC TTCTTC TTATTCTC TCTTTT- TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TT-TT-TC T-TTTTC TTTTTC TTTTTC
1555586 -TTTTC -TTTT- TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTT
1555606 TTCTTCAAGC
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
5 25 0.48
6 19 0.37
7 2 0.04
8 5 0.10
9 1 0.02
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:1555606 original size:23 final size:23
Alignment explanation
Indices: 1555539--1555610 Score: 85
Period size: 23 Copynumber: 3.1 Consensus size: 23
1555529 TGATCCCTTT
* *
1555539 TTTTCTTTTTTTTTCTTCTTCTTA
1 TTTTCTTTTTTTTTCTT-TTTTTC
1555563 TTCTCTCTTTTTTTTTC--TTTTTC
1 TT-T-TCTTTTTTTTTCTTTTTTTC
1555586 TTTTCTTTTTTTTTCTTTTTTTC
1 TTTTCTTTTTTTTTCTTTTTTTC
1555609 TT
1 TT
1555611 CAAGCATAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
21 12 0.29
22 1 0.02
23 14 0.33
24 2 0.05
25 1 0.02
26 12 0.29
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.82
Consensus pattern (23 bp):
TTTTCTTTTTTTTTCTTTTTTTC
Found at i:1562847 original size:16 final size:17
Alignment explanation
Indices: 1562821--1562886 Score: 79
Period size: 16 Copynumber: 4.2 Consensus size: 17
1562811 ATACATAAAG
1562821 AAAAT-AATGTAATG-A
1 AAAATGAATGTAATGCA
*
1562836 ATAATGAATGT-ATGCA
1 AAAATGAATGTAATGCA
1562852 AAAATGAATGT-ATGCA
1 AAAATGAATGTAATGCA
*
1562868 AAAATGCATGT-ATGCA
1 AAAATGAATGTAATGCA
1562884 AAA
1 AAA
1562887 GGTATTGATC
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
15 7 0.15
16 39 0.85
ACGTcount: A:0.52, C:0.06, G:0.17, T:0.26
Consensus pattern (17 bp):
AAAATGAATGTAATGCA
Found at i:1562862 original size:32 final size:31
Alignment explanation
Indices: 1562821--1562886 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 31
1562811 ATACATAAAG
*
1562821 AAAATAATGTAATG-AATAATGAATGTATGCA
1 AAAATAATGT-ATGCAAAAATGAATGTATGCA
*
1562852 AAAATGAATGTATGCAAAAATGCATGTATGCA
1 AAAAT-AATGTATGCAAAAATGAATGTATGCA
1562884 AAA
1 AAA
1562887 GGTATTGATC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 8 0.26
32 23 0.74
ACGTcount: A:0.52, C:0.06, G:0.17, T:0.26
Consensus pattern (31 bp):
AAAATAATGTATGCAAAAATGAATGTATGCA
Found at i:1566956 original size:20 final size:19
Alignment explanation
Indices: 1566917--1566968 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
1566907 TTTCTTTGAT
1566917 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
1566936 ATTAAAATAATTAATATATA
1 ATTAAAA-AATAAATAAATA
*
1566956 ATTTATAAAATAA
1 A-TTAAAAAATAA
1566969 GATATTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:1567151 original size:3 final size:3
Alignment explanation
Indices: 1567143--1567178 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1567133 TTTATGGTTA
*
1567143 AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1567179 TAAAAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1567224 original size:24 final size:24
Alignment explanation
Indices: 1567174--1567224 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
1567164 AATAGTAATA
* *
1567174 ATAATTAAAAATAAACATTAACAT
1 ATAACTAAAAATAAACATTAAAAT
*
1567198 ATAACTAACAATAAA-ATTAAAACT
1 ATAACTAAAAATAAACATTAAAA-T
1567222 ATA
1 ATA
1567225 TATATAACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (24 bp):
ATAACTAAAAATAAACATTAAAAT
Found at i:1568533 original size:3 final size:3
Alignment explanation
Indices: 1568525--1568584 Score: 72
Period size: 3 Copynumber: 20.7 Consensus size: 3
1568515 GGCTTGTTTG
* *
1568525 TAA TAA TAA TAA TAT TAA TAA TAA AAA TATA TAA TAA -AA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
1568569 T-A TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
1568585 TAAATAAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 6 0.12
3 41 0.82
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1568545 original size:15 final size:15
Alignment explanation
Indices: 1568525--1568591 Score: 82
Period size: 15 Copynumber: 4.4 Consensus size: 15
1568515 GGCTTGTTTG
1568525 TAATAATAATAATAT
1 TAATAATAATAATAT
*
1568540 TAATAATAAAAATAT
1 TAATAATAATAATAT
*
1568555 ATAATAAAAAATAATA-
1 -TAAT-AATAATAATAT
1568571 TAATAATAATAATAT
1 TAATAATAATAATAT
*
1568586 AAATAA
1 TAATAA
1568592 AATCGGGACA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
14 9 0.20
15 23 0.52
16 4 0.09
17 8 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAATAATAATAATAT
Found at i:1573040 original size:442 final size:442
Alignment explanation
Indices: 1572210--1573096 Score: 1504
Period size: 442 Copynumber: 2.0 Consensus size: 442
1572200 CCAAATGGTT
**
1572210 GGTCATTATCACTGCTAATGATTTTACTTGTTAAGAGTTTGATCATCATAAAGAAAGATGTGAAT
1 GGTCATTATCACTGCTAATGATTTTACTTGTTAAGAGTTTGATCATCATAAAGAAAGATGCAAAT
* *
1572275 TCTTTGCTTTGAAGATTTGGAGGCACTACTTATTCGGGGAGAAATGTCGCATCTTCACGGATTAC
66 TCTTTGCTTTGAAGATTTGGAGGCACTACTTATTCGGGGAGAAATGTCACATCTTCACGGATCAC
* *
1572340 AAGAGCCTTAAGTATCTACTTACTCAGAAAGAGTTCAACTTGAGGCAACGAAAATGGGTAGAGCT
131 AAGAGCCTTAAGTATCTACTAACTCAGAAAGAGTTCAACTTGAGGCAACGAAAATGGGTAGAACT
*
1572405 TTTGAATGACTATGATTGTGTGATCAATTATCATTCGGGTAAAGCAAACATTGTGGTAGACGCTT
196 TTTGAATGACTATGATTGTGTGATCAACTATCATTCGGGTAAAGCAAACATTGTGGTAGACGCTT
* * * *
1572470 TGAGCAGGAAGACCGTAATAGAGCTGAGAGCTTTACTATCACATCTAAGTTTGACTGATTTCAGT
261 TAAGAAGGAAGACCGTAATAGAGCTGAGAGCTTTACTAGCACATCTAAGTTCGACTGATTTCAGT
* * *
1572535 TGTTCGTTAGCCAAGTTAAGGGTCGAACCCTAGCTAGTAGGCGAAGTTAAGAGATTGCAAGGTTT
326 TGTTCGTTAGCCAAGTTAAGGGTCAAACCCTAGCTAGTAGGCGAAGTTAAGAGATTACAAGGTTC
*
1572600 GGATGACCAATTAAAGGCCTAAGTAGAGAAAGTCCTCCGAGGAGAGGCCCCA
391 GGATGACCAATTAAAGGCCTAAGTAGAGAAAGTCCTCCGACGAGAGGCCCCA
* *
1572652 GGTCATTATCACTGGTAATGATTTTATTTGTTAAGAGTTTGATCATCATAAAGAAAGATGCAAAT
1 GGTCATTATCACTGCTAATGATTTTACTTGTTAAGAGTTTGATCATCATAAAGAAAGATGCAAAT
* *
1572717 TTTTTTCTTTGAAGATTTGGAGGCACTACTTATTCGGGGAGAAATGTCACATCTTCACGGATCAC
66 TCTTTGCTTTGAAGATTTGGAGGCACTACTTATTCGGGGAGAAATGTCACATCTTCACGGATCAC
* *
1572782 AAGAGCCTTAAGTATTTACTAACTCAGAAAGAGTTCAACTTGAGGCAACGAAGATGGGTAGAACT
131 AAGAGCCTTAAGTATCTACTAACTCAGAAAGAGTTCAACTTGAGGCAACGAAAATGGGTAGAACT
* *
1572847 TTTGAATGATTATGATTGTGTGATCAACTATCATTCGGGTAAAGCGAACATTGTGGTAGACGCTT
196 TTTGAATGACTATGATTGTGTGATCAACTATCATTCGGGTAAAGCAAACATTGTGGTAGACGCTT
* *
1572912 TAAGAAGGAAGAGCGTAATAGAGCTGAGAGCTTTACTAGCACGTCTAAGTTCGACTGATTTCAGT
261 TAAGAAGGAAGACCGTAATAGAGCTGAGAGCTTTACTAGCACATCTAAGTTCGACTGATTTCAGT
*
1572977 TGTTTGTTAGCCAAGTTAAGGGTCAAACCCTAGCTAGTAGGCGAAGTTAAGAGATTACAAGGTTC
326 TGTTCGTTAGCCAAGTTAAGGGTCAAACCCTAGCTAGTAGGCGAAGTTAAGAGATTACAAGGTTC
* * * *
1573042 GGATGACCGATTAAAGGCCTAAGTAGAGCAAGTCCTCTGACGAGAGGGCCCA
391 GGATGACCAATTAAAGGCCTAAGTAGAGAAAGTCCTCCGACGAGAGGCCCCA
1573094 GGT
1 GGT
1573097 TTTGATTTAC
Statistics
Matches: 415, Mismatches: 30, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
442 415 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (442 bp):
GGTCATTATCACTGCTAATGATTTTACTTGTTAAGAGTTTGATCATCATAAAGAAAGATGCAAAT
TCTTTGCTTTGAAGATTTGGAGGCACTACTTATTCGGGGAGAAATGTCACATCTTCACGGATCAC
AAGAGCCTTAAGTATCTACTAACTCAGAAAGAGTTCAACTTGAGGCAACGAAAATGGGTAGAACT
TTTGAATGACTATGATTGTGTGATCAACTATCATTCGGGTAAAGCAAACATTGTGGTAGACGCTT
TAAGAAGGAAGACCGTAATAGAGCTGAGAGCTTTACTAGCACATCTAAGTTCGACTGATTTCAGT
TGTTCGTTAGCCAAGTTAAGGGTCAAACCCTAGCTAGTAGGCGAAGTTAAGAGATTACAAGGTTC
GGATGACCAATTAAAGGCCTAAGTAGAGAAAGTCCTCCGACGAGAGGCCCCA
Found at i:1575183 original size:18 final size:18
Alignment explanation
Indices: 1575116--1575174 Score: 91
Period size: 18 Copynumber: 3.3 Consensus size: 18
1575106 AGGGTTCTAC
1575116 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
* *
1575134 GTGGTCCTTCGGGATACA
1 GTGGTCCTTCGGGACATA
*
1575152 GTGATCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
1575170 GTGGT
1 GTGGT
1575175 TCTACGGGAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.17, C:0.20, G:0.34, T:0.29
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:1583901 original size:94 final size:94
Alignment explanation
Indices: 1583740--1583927 Score: 376
Period size: 94 Copynumber: 2.0 Consensus size: 94
1583730 ATAAGCTTGT
1583740 GGGGAGAGTTATCTGGAAAACTCTTCTCCCTTCTTCTTCCTCCTCCACGTGAGAGCTCAAGCAAA
1 GGGGAGAGTTATCTGGAAAACTCTTCTCCCTTCTTCTTCCTCCTCCACGTGAGAGCTCAAGCAAA
1583805 GGTAAGATTTCTTGTTGTTGATTATTAGC
66 GGTAAGATTTCTTGTTGTTGATTATTAGC
1583834 GGGGAGAGTTATCTGGAAAACTCTTCTCCCTTCTTCTTCCTCCTCCACGTGAGAGCTCAAGCAAA
1 GGGGAGAGTTATCTGGAAAACTCTTCTCCCTTCTTCTTCCTCCTCCACGTGAGAGCTCAAGCAAA
1583899 GGTAAGATTTCTTGTTGTTGATTATTAGC
66 GGTAAGATTTCTTGTTGTTGATTATTAGC
1583928 TGAAATTTAA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 94 1.00
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.34
Consensus pattern (94 bp):
GGGGAGAGTTATCTGGAAAACTCTTCTCCCTTCTTCTTCCTCCTCCACGTGAGAGCTCAAGCAAA
GGTAAGATTTCTTGTTGTTGATTATTAGC
Found at i:1585112 original size:39 final size:39
Alignment explanation
Indices: 1585069--1585147 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
1585059 GCTACCTGAT
1585069 TACAGGTACATATGAAAGAAGTTATGAGTTTATAAGAAC
1 TACAGGTACATATGAAAGAAGTTATGAGTTTATAAGAAC
1585108 TACAGGTACATATGAAAGAAGTTATGAGTTTATAAGAAC
1 TACAGGTACATATGAAAGAAGTTATGAGTTTATAAGAAC
1585147 T
1 T
1585148 TGTGATATGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.43, C:0.08, G:0.20, T:0.29
Consensus pattern (39 bp):
TACAGGTACATATGAAAGAAGTTATGAGTTTATAAGAAC
Found at i:1587563 original size:179 final size:176
Alignment explanation
Indices: 1587263--1587617 Score: 674
Period size: 179 Copynumber: 2.0 Consensus size: 176
1587253 CATGTCATAC
1587263 ACACATGCAACATACCTTCTTGTATTACTTTCACTTTCATTTGTCTTTCAATTGCATTGCCCATG
1 ACACATGCAACATACCTTCTTGTATTACTTTCACTTTCATTTGTCTTTCAATTGCATTGCCCATG
1587328 TATATTATTATCATTATCAACATCATTATAATTCAGGCAACACATGTCATATCACCAAAAGTATA
66 TATATTATTATCATTATCAACATCATTATAATTCAGGCAACACATGTCATATCACCAAAAGTATA
1587393 TACATCACATATATTGTATTTGTTATTGTCTCTTTATTCGCCCATGATA
131 T--A-CACATATATTGTATTTGTTATTGTCTCTTTATTCGCCCATGATA
1587442 ACACATGCAACATACCTTCTTGTATTACTTTCACTTTCATTTGTCTTTCAATTGCATTGCCCATG
1 ACACATGCAACATACCTTCTTGTATTACTTTCACTTTCATTTGTCTTTCAATTGCATTGCCCATG
*
1587507 TATATTATTATCTTTATCAACATCATTATAATTCAGGCAACACATGTCATATCACCAAAAGTATA
66 TATATTATTATCATTATCAACATCATTATAATTCAGGCAACACATGTCATATCACCAAAAGTATA
1587572 TACACATATATTGTATTTGTTATTGTCTCTTTATTCGCCCATGATA
131 TACACATATATTGTATTTGTTATTGTCTCTTTATTCGCCCATGATA
1587618 CCTACGTGTA
Statistics
Matches: 175, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
176 44 0.25
177 1 0.01
179 130 0.74
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.41
Consensus pattern (176 bp):
ACACATGCAACATACCTTCTTGTATTACTTTCACTTTCATTTGTCTTTCAATTGCATTGCCCATG
TATATTATTATCATTATCAACATCATTATAATTCAGGCAACACATGTCATATCACCAAAAGTATA
TACACATATATTGTATTTGTTATTGTCTCTTTATTCGCCCATGATA
Found at i:1588065 original size:31 final size:31
Alignment explanation
Indices: 1588027--1588120 Score: 163
Period size: 31 Copynumber: 3.0 Consensus size: 31
1588017 CCCGAAGGAC
*
1588027 CAGTCCATA-GATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1588058 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1588089 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1588120 C
1 C
1588121 CCTCGACCCT
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 60 0.98
32 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.18
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1588910 original size:64 final size:64
Alignment explanation
Indices: 1588774--1588930 Score: 156
Period size: 64 Copynumber: 2.5 Consensus size: 64
1588764 TGATAAAGGT
* * * * ** *
1588774 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGTATTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAATGCATTCGATGTTGTATTATTAAAGAG
* * * *
1588838 ATGTATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTATTTATT-TTAAA-AG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAATGCATTCGATGT-TGTATTATTAAAGAG
* * *
1588901 AGTGCATCGATGCACTTCATGTGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
1588931 ACACCTTCAA
Statistics
Matches: 76, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
63 2 0.03
64 69 0.91
65 5 0.07
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAAATGCATTCGATGTTGTATTATTAAAGAG
Found at i:1592435 original size:5 final size:5
Alignment explanation
Indices: 1592425--1592452 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1592415 TTCAAGCATG
1592425 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1592453 TTATTTTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:1593764 original size:19 final size:18
Alignment explanation
Indices: 1593720--1593768 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
1593710 AAATATTGAA
*
1593720 CGAAAAAAAATAGCAGTT
1 CGAAAAAAAAAAGCAGTT
*
1593738 C-AAAAAAAAAAGCTGTT
1 CGAAAAAAAAAAGCAGTT
1593755 CGAAAGAAAAAAAG
1 CGAAA-AAAAAAAG
1593769 AGAAAAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 15 0.56
18 4 0.15
19 8 0.30
ACGTcount: A:0.61, C:0.10, G:0.16, T:0.12
Consensus pattern (18 bp):
CGAAAAAAAAAAGCAGTT
Found at i:1596221 original size:18 final size:18
Alignment explanation
Indices: 1596198--1596265 Score: 91
Period size: 18 Copynumber: 3.8 Consensus size: 18
1596188 AGGGTTCTAC
1596198 GTGGTCCTTCGGGATATA
1 GTGGTCCTTCGGGATATA
* *
1596216 GTGGTCCTTCTGGATACA
1 GTGGTCCTTCGGGATATA
* *
1596234 GTGATCCTTCGGGACATA
1 GTGGTCCTTCGGGATATA
*
1596252 GTGGTCCTACGGGA
1 GTGGTCCTTCGGGA
1596266 CAAATTCTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.18, C:0.21, G:0.32, T:0.29
Consensus pattern (18 bp):
GTGGTCCTTCGGGATATA
Found at i:1596993 original size:86 final size:82
Alignment explanation
Indices: 1596852--1597019 Score: 300
Period size: 86 Copynumber: 2.0 Consensus size: 82
1596842 CAGATCAGAA
1596852 ATATTTTGTAAAGTATGTTGTCATAATTTAGTATGTTGGCATGTAACTAAGTTATTATATATGTA
1 ATATTTTGTAAAGTATGTTGTCATAATTTAGTATGTTGGCATGTAACTAAGTTATTATATATGTA
1596917 TGCTCTGATGGAGTTTG
66 TGCTCTGATGGAGTTTG
1596934 ATATTTTGTAAAGTATGTCTTGTCATATAATTTAGTATGTTGGCATGTAACTAAGTTATTATATA
1 ATATTTTGTAAAGTATG--TTGTC--ATAATTTAGTATGTTGGCATGTAACTAAGTTATTATATA
1596999 TGTATGCTCTGATGGAGTTTG
62 TGTATGCTCTGATGGAGTTTG
1597020 TTAAGGTTTT
Statistics
Matches: 82, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
82 17 0.21
84 5 0.06
86 60 0.73
ACGTcount: A:0.28, C:0.07, G:0.20, T:0.45
Consensus pattern (82 bp):
ATATTTTGTAAAGTATGTTGTCATAATTTAGTATGTTGGCATGTAACTAAGTTATTATATATGTA
TGCTCTGATGGAGTTTG
Found at i:1598127 original size:4 final size:4
Alignment explanation
Indices: 1598120--1598145 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1598110 TATATATATA
1598120 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
1598146 GAAAATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:1598280 original size:50 final size:50
Alignment explanation
Indices: 1598221--1598363 Score: 214
Period size: 51 Copynumber: 2.8 Consensus size: 50
1598211 GAGATATACA
1598221 TACTTACACCAGTGTAAGTATGTGTTAAGTGTTACACTTTTTATTTTATT
1 TACTTACACCAGTGTAAGTATGTGTTAAGTGTTACACTTTTTATTTTATT
*
1598271 TACTTACACCAGTATAAGTATGTGTTAAGTGTTACACTTGTTTATTTTATT
1 TACTTACACCAGTGTAAGTATGTGTTAAGTGTTACACTT-TTTATTTTATT
* ** * * *
1598322 CACTTACACTGGTGTAAATATGTGTTAAGTGCTACATTTTTT
1 TACTTACACCAGTGTAAGTATGTGTTAAGTGTTACACTTTTT
1598364 GTAGTATGAA
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
50 41 0.49
51 43 0.51
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.46
Consensus pattern (50 bp):
TACTTACACCAGTGTAAGTATGTGTTAAGTGTTACACTTTTTATTTTATT
Found at i:1603576 original size:19 final size:19
Alignment explanation
Indices: 1603552--1603609 Score: 116
Period size: 19 Copynumber: 3.1 Consensus size: 19
1603542 GAAATTAAAG
1603552 ATAGTGCCATTAGAAGAGA
1 ATAGTGCCATTAGAAGAGA
1603571 ATAGTGCCATTAGAAGAGA
1 ATAGTGCCATTAGAAGAGA
1603590 ATAGTGCCATTAGAAGAGA
1 ATAGTGCCATTAGAAGAGA
1603609 A
1 A
1603610 ACAGAAGGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.43, C:0.10, G:0.26, T:0.21
Consensus pattern (19 bp):
ATAGTGCCATTAGAAGAGA
Found at i:1605076 original size:61 final size:60
Alignment explanation
Indices: 1605001--1605122 Score: 190
Period size: 61 Copynumber: 2.0 Consensus size: 60
1604991 TTGTTTCGTG
* *
1605001 CTGCTAATTACAGGGAAAGGATTGCAGATGTCGCATTCCAAATCTTAAGACTCGAAACGAT
1 CTGCTAATTACAGGGAAAGGATTGCAGATGTCACAAT-CAAATCTTAAGACTCGAAACGAT
* * *
1605062 CTGCTAATTGCAGGGAAAGGATTGCAGATGTCATAATCAAATCTTAAGACTCGAATCGAT
1 CTGCTAATTACAGGGAAAGGATTGCAGATGTCACAATCAAATCTTAAGACTCGAAACGAT
1605122 C
1 C
1605123 GATGGCATCC
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
60 23 0.41
61 33 0.59
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.25
Consensus pattern (60 bp):
CTGCTAATTACAGGGAAAGGATTGCAGATGTCACAATCAAATCTTAAGACTCGAAACGAT
Found at i:1607244 original size:127 final size:127
Alignment explanation
Indices: 1607013--1607271 Score: 509
Period size: 127 Copynumber: 2.0 Consensus size: 127
1607003 TTTAATTGGA
*
1607013 AAAAGGGCTAGTTTTCAAGTTGTGAGAATTGTAGGACATTATTGAATAAATGTGCAATTTGAGGT
1 AAAATGGCTAGTTTTCAAGTTGTGAGAATTGTAGGACATTATTGAATAAATGTGCAATTTGAGGT
1607078 ACTCAAAGTTAATTTATAATGATTATATGCTGGAATTTTAAGTTAGGGAGTTGTTTGGAACC
66 ACTCAAAGTTAATTTATAATGATTATATGCTGGAATTTTAAGTTAGGGAGTTGTTTGGAACC
1607140 AAAATGGCTAGTTTTCAAGTTGTGAGAATTGTAGGACATTATTGAATAAATGTGCAATTTGAGGT
1 AAAATGGCTAGTTTTCAAGTTGTGAGAATTGTAGGACATTATTGAATAAATGTGCAATTTGAGGT
1607205 ACTCAAAGTTAATTTATAATGATTATATGCTGGAATTTTAAGTTAGGGAGTTGTTTGGAACC
66 ACTCAAAGTTAATTTATAATGATTATATGCTGGAATTTTAAGTTAGGGAGTTGTTTGGAACC
1607267 AAAAT
1 AAAAT
1607272 ACAAATTTGG
Statistics
Matches: 131, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
127 131 1.00
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (127 bp):
AAAATGGCTAGTTTTCAAGTTGTGAGAATTGTAGGACATTATTGAATAAATGTGCAATTTGAGGT
ACTCAAAGTTAATTTATAATGATTATATGCTGGAATTTTAAGTTAGGGAGTTGTTTGGAACC
Found at i:1610211 original size:22 final size:21
Alignment explanation
Indices: 1610168--1610211 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1610158 TATATGAATT
*
1610168 AAAATTTGAAATAATATTAAA
1 AAAATTTGAAATAATATAAAA
*
1610189 AAAATATTGAAAT-AGATAAAA
1 AAAAT-TTGAAATAATATAAAA
1610210 AA
1 AA
1610212 TTAAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (21 bp):
AAAATTTGAAATAATATAAAA
Found at i:1611363 original size:20 final size:22
Alignment explanation
Indices: 1611338--1611377 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1611328 AGTCATATAT
1611338 AGCCG-TTGGGGA-TGTTTTGG
1 AGCCGTTTGGGGATTGTTTTGG
1611358 AGCCGTTTGGGGATTGTTTT
1 AGCCGTTTGGGGATTGTTTT
1611378 TCTGTAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 7 0.39
22 6 0.33
ACGTcount: A:0.10, C:0.10, G:0.40, T:0.40
Consensus pattern (22 bp):
AGCCGTTTGGGGATTGTTTTGG
Found at i:1611536 original size:36 final size:36
Alignment explanation
Indices: 1611489--1611557 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
1611479 TTGCAGCCTT
*
1611489 AGTGTATGGATACACT-GTAGGGTGTATCGGTACACC
1 AGTGTATGGATACACTCATAGGG-GTATCGGTACACC
1611525 AGTGTATGGATACACTCATAGGGGTATCGGTAC
1 AGTGTATGGATACACTCATAGGGGTATCGGTAC
1611558 CCTTTTTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
36 26 0.84
37 5 0.16
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (36 bp):
AGTGTATGGATACACTCATAGGGGTATCGGTACACC
Found at i:1611860 original size:21 final size:19
Alignment explanation
Indices: 1611836--1611893 Score: 82
Period size: 18 Copynumber: 3.0 Consensus size: 19
1611826 ATGTTTAATG
*
1611836 AAAAAGATATCATTTGTTA
1 AAAAAGATATCAATTGTTA
1611855 ACAAAAGGATATCAATTGTT-
1 A-AAAA-GATATCAATTGTTA
1611875 AAAAAGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
1611894 CCAATTGTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
18 13 0.37
19 5 0.14
20 5 0.14
21 12 0.34
ACGTcount: A:0.48, C:0.07, G:0.12, T:0.33
Consensus pattern (19 bp):
AAAAAGATATCAATTGTTA
Found at i:1614684 original size:36 final size:35
Alignment explanation
Indices: 1614635--1614703 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 35
1614625 TTGCAACCAG
*
1614635 AGTGTATGTATACACTGC-AGGGTGTATCGGTACACC
1 AGTGTATGGATACACT-CAAGGG-GTATCGGTACACC
1614671 AGTGTATGGATACACTCATAGGGGTATCGGTAC
1 AGTGTATGGATACACTCA-AGGGGTATCGGTAC
1614704 CCCTTTTTGC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 1 0.03
36 25 0.83
37 4 0.13
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (35 bp):
AGTGTATGGATACACTCAAGGGGTATCGGTACACC
Found at i:1614799 original size:20 final size:20
Alignment explanation
Indices: 1614736--1614805 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
1614726 AGCAGTCATA
1614736 GGTGTATGGATACAACTGCAG
1 GGTGTATGGATAC-ACTGCAG
1614757 GGTGTATCGG-TACAC--CA-
1 GGTGTAT-GGATACACTGCAG
1614774 -GTGTATGGATACACTGCAG
1 GGTGTATGGATACACTGCAG
1614793 GGTGTATGGATAC
1 GGTGTATGGATAC
1614806 CTTTTAGCAT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
15 2 0.05
16 11 0.26
18 4 0.09
20 14 0.33
21 10 0.23
22 2 0.05
ACGTcount: A:0.26, C:0.16, G:0.33, T:0.26
Consensus pattern (20 bp):
GGTGTATGGATACACTGCAG
Found at i:1615670 original size:21 final size:21
Alignment explanation
Indices: 1615624--1615673 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1615614 CTTAGGGAAT
*
1615624 CGATTCCCTATTAGAGGAAAC
1 CGATTCCCTATGAGAGGAAAC
* **
1615645 TGATTCCCTATGAGAGGGTAC
1 CGATTCCCTATGAGAGGAAAC
1615666 CGATTCCC
1 CGATTCCC
1615674 CCACACTCGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (21 bp):
CGATTCCCTATGAGAGGAAAC
Found at i:1615868 original size:13 final size:13
Alignment explanation
Indices: 1615847--1615901 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
1615837 AAGTTCGATA
*
1615847 AATTCAAATACTT
1 AATTGAAATACTT
1615860 AATTGAAATACTT
1 AATTGAAATACTT
* *
1615873 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
1615887 AATTGAAATACTT
1 AATTGAAATACTT
1615900 AA
1 AA
1615902 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:1615942 original size:32 final size:33
Alignment explanation
Indices: 1615887--1615984 Score: 132
Period size: 32 Copynumber: 3.0 Consensus size: 33
1615877 AACTCAACAT
* *
1615887 AATTGAAATACTTAAATACTTCCAAGTTTTGATA
1 AATTCAAATACTTAAA-ACTTCCAAGTTTCGATA
1615921 AATTCAAA-ACTTAAAACTTCCAAG-TTCGATA
1 AATTCAAATACTTAAAACTTCCAAGTTTCGATA
1615952 AATTCAAATACTTAAAAACTT-CAAG-TTCGATA
1 AATTCAAATACTT-AAAACTTCCAAGTTTCGATA
1615984 A
1 A
1615985 TTGAAACAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
31 14 0.23
32 25 0.42
33 14 0.23
34 7 0.12
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (33 bp):
AATTCAAATACTTAAAACTTCCAAGTTTCGATA
Found at i:1616003 original size:21 final size:21
Alignment explanation
Indices: 1615979--1616018 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1615969 ACTTCAAGTT
1615979 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
1616000 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
1616019 ATAAAATACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:1616036 original size:27 final size:27
Alignment explanation
Indices: 1615998--1616053 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1615988 AAACAAAGTT
1615998 TACGATAATTGAAATAAAGTTATAAAA
1 TACGATAATTGAAATAAAGTTATAAAA
1616025 TACGATAATTGAAATAAAGTTATAAAA
1 TACGATAATTGAAATAAAGTTATAAAA
1616052 TA
1 TA
1616054 AACTACATTG
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:0.55, C:0.04, G:0.11, T:0.30
Consensus pattern (27 bp):
TACGATAATTGAAATAAAGTTATAAAA
Found at i:1618501 original size:28 final size:29
Alignment explanation
Indices: 1618469--1618527 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
1618459 AAAAAACCGG
*
1618469 TTTTTC-CCAAATCCGAT-TTCGGATATTT
1 TTTTTCACAAAATCCGATATTCGGAT-TTT
*
1618497 TTTTTCACAAAATCGGATATTCGGATTTT
1 TTTTTCACAAAATCCGATATTCGGATTTT
1618526 TT
1 TT
1618528 GTGCACCCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 6 0.22
29 14 0.52
30 7 0.26
ACGTcount: A:0.24, C:0.17, G:0.12, T:0.47
Consensus pattern (29 bp):
TTTTTCACAAAATCCGATATTCGGATTTT
Done.