Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015381.1 Kokia drynarioides strain JFW-HI SEQ_130428, 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: 2291099
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 587 characters in sequence are not A, C, G, or T
File 7 of 8
Found at i:1693757 original size:32 final size:32
Alignment explanation
Indices: 1693719--1693783 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
1693709 TTATTCATCT
*
1693719 ATCACTGTTCATCTTTTACTTTCATTTCAATC
1 ATCACTGTTCATCTTATACTTTCATTTCAATC
1693751 ATCACTGTTCATCTTATACTTTCATTTCAATC
1 ATCACTGTTCATCTTATACTTTCATTTCAATC
1693783 A
1 A
1693784 ATCTTATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.25, G:0.03, T:0.48
Consensus pattern (32 bp):
ATCACTGTTCATCTTATACTTTCATTTCAATC
Found at i:1705298 original size:12 final size:11
Alignment explanation
Indices: 1705277--1705309 Score: 57
Period size: 12 Copynumber: 2.9 Consensus size: 11
1705267 TAGTCACTTA
1705277 AAAAGAAAAAG
1 AAAAGAAAAAG
1705288 AAAAGAGAAAAG
1 AAAAGA-AAAAG
1705300 AAAAGAAAAA
1 AAAAGAAAAA
1705310 TTAATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:1711618 original size:43 final size:43
Alignment explanation
Indices: 1711563--1711646 Score: 159
Period size: 43 Copynumber: 2.0 Consensus size: 43
1711553 CAGTGCAACA
1711563 ATTAAAGGAATGATATTCTAGGATCTTTAGCTATATTAGTGCG
1 ATTAAAGGAATGATATTCTAGGATCTTTAGCTATATTAGTGCG
*
1711606 ATTAAAGGAATGATATTTTAGGATCTTTAGCTATATTAGTG
1 ATTAAAGGAATGATATTCTAGGATCTTTAGCTATATTAGTG
1711647 GATGTATTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.39
Consensus pattern (43 bp):
ATTAAAGGAATGATATTCTAGGATCTTTAGCTATATTAGTGCG
Found at i:1711734 original size:2 final size:2
Alignment explanation
Indices: 1711727--1711752 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1711717 GGAATCTTGG
1711727 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
1711753 TGAGGTCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1712267 original size:62 final size:63
Alignment explanation
Indices: 1712167--1712294 Score: 208
Period size: 62 Copynumber: 2.0 Consensus size: 63
1712157 GACATAAGGT
*
1712167 AGTGCTTCTCCATTAGGAATGGAACGAGAGTGCAACAATTGAGATCAGATTTGATGAACTGTA
1 AGTGCTTCTCCATTAGGAATGGAACGAGAGTGCAACAATTGAGATCAGATTTGATGAACTATA
1712230 AGTGCTTCTCCATT-GGTAA-GG-ACTGAGAGTGCAACAATTGAGATCAGATTTGATGAACTATA
1 AGTGCTTCTCCATTAGG-AATGGAAC-GAGAGTGCAACAATTGAGATCAGATTTGATGAACTATA
1712292 AGT
1 AGT
1712295 TGGATGGACA
Statistics
Matches: 62, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
61 2 0.03
62 44 0.71
63 16 0.26
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (63 bp):
AGTGCTTCTCCATTAGGAATGGAACGAGAGTGCAACAATTGAGATCAGATTTGATGAACTATA
Found at i:1714280 original size:24 final size:24
Alignment explanation
Indices: 1714261--1714382 Score: 181
Period size: 24 Copynumber: 5.1 Consensus size: 24
1714251 AGAGTTTGAC
1714261 TGAAACAAATAAATAAAGTTTAAT
1 TGAAACAAATAAATAAAGTTTAAT
* * *
1714285 TAAAACAAATAAACAGAGTTTAAT
1 TGAAACAAATAAATAAAGTTTAAT
1714309 TGAAACAAATAAATAAAGTTTAAT
1 TGAAACAAATAAATAAAGTTTAAT
* *
1714333 TGAAACAAATAAACAAATTTTAAT
1 TGAAACAAATAAATAAAGTTTAAT
* *
1714357 TGAATCAAATAAATAGAGTTTAAT
1 TGAAACAAATAAATAAAGTTTAAT
1714381 TG
1 TG
1714383 GAAGATTATT
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 86 1.00
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.30
Consensus pattern (24 bp):
TGAAACAAATAAATAAAGTTTAAT
Found at i:1716235 original size:24 final size:25
Alignment explanation
Indices: 1716208--1716270 Score: 105
Period size: 24 Copynumber: 2.6 Consensus size: 25
1716198 AGTCTAAACT
1716208 AATAAGAGTTTAATTGAAAC-AATA
1 AATAAGAGTTTAATTGAAACAAATA
1716232 AAT-AGAGTTTAATTGAAACAAATA
1 AATAAGAGTTTAATTGAAACAAATA
1716256 AA-AAGAGTTTAATTG
1 AATAAGAGTTTAATTG
1716271 TAAGATTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
23 16 0.43
24 21 0.57
ACGTcount: A:0.52, C:0.03, G:0.14, T:0.30
Consensus pattern (25 bp):
AATAAGAGTTTAATTGAAACAAATA
Found at i:1716938 original size:21 final size:21
Alignment explanation
Indices: 1716922--1716966 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1716912 CAATATGGTT
*
1716922 ATATGAATCGGTTATATGGAA
1 ATATGAATCAGTTATATGGAA
*
1716943 ATATGAGTCAGTTATATGGAA
1 ATATGAATCAGTTATATGGAA
1716964 ATA
1 ATA
1716967 ATCATATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.04, G:0.22, T:0.33
Consensus pattern (21 bp):
ATATGAATCAGTTATATGGAA
Found at i:1717197 original size:36 final size:36
Alignment explanation
Indices: 1717156--1717224 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
1717146 TGTAAACTCA
*
1717156 CTAACCTTGTGAGACTTGTGATGTATATAGGTATCG
1 CTAACCTTGTGAGACTGGTGATGTATATAGGTATCG
1717192 CTAACCTTGTGAGACTGGTGATGTATATAGGTA
1 CTAACCTTGTGAGACTGGTGATGTATATAGGTA
1717225 ATTAATGAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (36 bp):
CTAACCTTGTGAGACTGGTGATGTATATAGGTATCG
Found at i:1718821 original size:238 final size:237
Alignment explanation
Indices: 1718384--1718854 Score: 782
Period size: 238 Copynumber: 2.0 Consensus size: 237
1718374 GAGAGATTTG
* * *
1718384 TCTGACATTTCCTATGTTCAGTTGAATTGCCAAATGGTGGAACAATTGTAGTACTAAAAGAAGGA
1 TCTGACATTTCCCATGTTCAGTTGAATTGCCAAATGGTGAAACAATTGTAGCACTAAAAGAAGGA
* *
1718449 ATGAGTCATCTTGGAGAAGGATTTAAGTTGCAACATATTCTTTTTGTGCCTAATTTAGAATACAA
66 ATGAGGCATCTTGGAGAAGGATTGAAGTTGCAACATATTCTTTTTGTGCCTAATTTAGAATACAA
*
1718514 TTTGATTTCTATTTCACAACTTCTTAATGACTCAAATATGGTACTGCAAATCACTAATAAAATAT
131 TTTGATTTCTATTTCACAACTTCTTAATGACTCAAACATGGTACTGCAAATCACTAATAAAATAT
* **
1718579 GTGTTATACATGACCGAAATATGAGGAGGCTGATTGGATCTA
196 GTGTTATACATGACCAAAATACAAGGAGGCTGATTGGATCTA
*
1718621 TCTGACATTATCCCATGTGT-AGTTGAATTGCTAAATGGTGAAACAATTGTAGCACTAAAAGAAG
1 TCTGACATT-TCCCATGT-TCAGTTGAATTGCCAAATGGTGAAACAATTGTAGCACTAAAAGAAG
* *
1718685 GACTGAGGCATCTTGGAGAAGGATTGGAGTTGCAACATATTCTTTTTGTGCCTAATTTAGAATAC
64 GAATGAGGCATCTTGGAGAAGGATTGAAGTTGCAACATATTCTTTTTGTGCCTAATTTAGAATAC
**
1718750 AATTTGATTTCTATTTCACAACTTCTTAATGACTCAAACATGGTGTTGCAAATCACTAATAAAAT
129 AATTTGATTTCTATTTCACAACTTCTTAATGACTCAAACATGGTACTGCAAATCACTAATAAAAT
*
1718815 ATGTGTTATACATGACTAAAATACAAGGAGGCTGATTGGA
194 ATGTGTTATACATGACCAAAATACAAGGAGGCTGATTGGA
1718855 GTGGGTGAAC
Statistics
Matches: 217, Mismatches: 15, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
237 9 0.04
238 207 0.95
239 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (237 bp):
TCTGACATTTCCCATGTTCAGTTGAATTGCCAAATGGTGAAACAATTGTAGCACTAAAAGAAGGA
ATGAGGCATCTTGGAGAAGGATTGAAGTTGCAACATATTCTTTTTGTGCCTAATTTAGAATACAA
TTTGATTTCTATTTCACAACTTCTTAATGACTCAAACATGGTACTGCAAATCACTAATAAAATAT
GTGTTATACATGACCAAAATACAAGGAGGCTGATTGGATCTA
Found at i:1728374 original size:43 final size:43
Alignment explanation
Indices: 1728295--1728378 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 43
1728285 TGGTGCAGCA
* * *
1728295 ATTAAAGGAATGATTTTCTAGGATCTTTAGCCATATTAGTGTG
1 ATTAAAGGAATGATATTCTAGAATCTTTAACCATATTAGTGTG
**
1728338 ATTAAAGGAATGATATTCTAGAATCTTTAATTATATTAGTG
1 ATTAAAGGAATGATATTCTAGAATCTTTAACCATATTAGTG
1728379 GATGCATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.40
Consensus pattern (43 bp):
ATTAAAGGAATGATATTCTAGAATCTTTAACCATATTAGTGTG
Found at i:1729103 original size:73 final size:73
Alignment explanation
Indices: 1729022--1729168 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
1729012 AGGTGAATGT
1729022 AGATAGTTTTGATAAATACTTAATCTGTCTTAAACAATTCTACTTATGATAAAAATTATATTATA
1 AGATAGTTTTGATAAATACTTAATCTGTCTTAAACAATTCTACTTATGATAAAAATTATATTATA
1729087 AATTATAC
66 AATTATAC
1729095 AGATAGTTTTGATAAATACTTAATCTGTCTTAAACAATTCTACTTATGATAAAAATTATATTATA
1 AGATAGTTTTGATAAATACTTAATCTGTCTTAAACAATTCTACTTATGATAAAAATTATATTATA
1729160 AATTATAC
66 AATTATAC
1729168 A
1 A
1729169 ATACTAAATT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.41
Consensus pattern (73 bp):
AGATAGTTTTGATAAATACTTAATCTGTCTTAAACAATTCTACTTATGATAAAAATTATATTATA
AATTATAC
Found at i:1730381 original size:21 final size:22
Alignment explanation
Indices: 1730357--1730412 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
1730347 CCTAACAAAC
* * *
1730357 AAGTTTCAAGACTTGAG-GAGT
1 AAGTTTCAAGACTTAAGCCAAT
* *
1730378 AAGTCTCAATACTTAAGCCAAT
1 AAGTTTCAAGACTTAAGCCAAT
1730400 AAGTTTCAAGACT
1 AAGTTTCAAGACT
1730413 ATATTGCTTT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
21 14 0.52
22 13 0.48
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (22 bp):
AAGTTTCAAGACTTAAGCCAAT
Found at i:1731618 original size:10 final size:10
Alignment explanation
Indices: 1731603--1731634 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
1731593 AAAATAAAGG
1731603 ATTATTTAAA
1 ATTATTTAAA
1731613 ATTATTT-AA
1 ATTATTTAAA
1731622 ATTATTTAAA
1 ATTATTTAAA
1731632 ATT
1 ATT
1731635 TAAGATTACG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
ATTATTTAAA
Found at i:1733326 original size:405 final size:404
Alignment explanation
Indices: 1732576--1733391 Score: 1569
Period size: 405 Copynumber: 2.0 Consensus size: 404
1732566 TGGTTCTTTG
* *
1732576 GGCCTACGTTATTTTTGTTCTTGAAAACGAGAAGAGAATGTCTTTACATCCAAAATAAGGATCAT
1 GGCCTACATTATTTTTGTTCTTGAAAACGAGAAAAGAATGTCTTTACATCCAAAATAAGGATCAT
*
1732641 GAAATCAAGCCCAAACCCCAAAATCAGTTGGAAACTGATTTCACCATAAAATATCCTAATCACTC
66 GAAATCAAGCCCAAACCCCAAAATCAATTGGAAACTGATTTCACCATAAAATATCCTAATCACTC
1732706 GGAGTCAATGAATGCATCGTTTAGACGCCAATGCTCATGCAAATACTAACATACATCATATGCAC
131 GGAGTCAATGAATGCATCGTTTAGACGCCAATGCTCATGCAAATACTAACATACATCATATGCAC
1732771 ATATACCATACATGCTTTTCACATCAGAACATACTAACAAATCATATGACAGATCATATACAAAT
196 ATATACCATACATGCTTTTCACATCAGAACATACTAACAAATCATATGACAGATCATATACAAAT
1732836 TTCATTTTAAACATACTTGCAATTGTAACACATACCTTATCCTTATTACGTACATTCACAAAATC
261 TTCATTTTAAACATACTTGCAATTGTAACACATACCTTATCCTTATTACGTACATTCACAAAATC
1732901 TCATATTTCATATTTAGAATCATATTTAAGCGAAACCGACCCCCATGAAAGGTCTAATTATGAAT
326 TCATATTTCATATTTAGAATCATATTTAAGCGAAACCGACCCCCATGAAAGGTCTAATTATGAAT
1732966 TTCATAGCCTAACA
391 TTCATAGCCTAACA
1732980 GGCCTACATTATTTTTGTTCTTGAAAACGAGAAAAGAATGTCTTTACATCCAAAATAAGGATCAT
1 GGCCTACATTATTTTTGTTCTTGAAAACGAGAAAAGAATGTCTTTACATCCAAAATAAGGATCAT
* *
1733045 GAAATCAAGCCTAAACCCCCAAAGTCAATTGGAAACTGATTTCACCATAAAATATCCTAATCACT
66 GAAATCAAGCCCAAA-CCCCAAAATCAATTGGAAACTGATTTCACCATAAAATATCCTAATCACT
1733110 CGGAGTCAATGAATGCATCGTTTAGACGCCAATGCTCATGCAAATACTAACATACATCATATGCA
130 CGGAGTCAATGAATGCATCGTTTAGACGCCAATGCTCATGCAAATACTAACATACATCATATGCA
*
1733175 CATATACCATACATGCTTTTCACATCAGAACATACTAACAAATCATATGACAGATCATGTACAAA
195 CATATACCATACATGCTTTTCACATCAGAACATACTAACAAATCATATGACAGATCATATACAAA
1733240 TTTCATTTTAAACATACTTGCAATTGTAACACATACCTTATCCTTATTACGTACATTCACAAAAT
260 TTTCATTTTAAACATACTTGCAATTGTAACACATACCTTATCCTTATTACGTACATTCACAAAAT
1733305 CTCATATTTCATATTTAGAATCATATTTAAGCGAAACCGACCCCCATGAAAGGTCTAATTATGAA
325 CTCATATTTCATATTTAGAATCATATTTAAGCGAAACCGACCCCCATGAAAGGTCTAATTATGAA
1733370 TTTCATAGCCTAACA
390 TTTCATAGCCTAACA
1733385 GGCCTAC
1 GGCCTAC
1733392 GTGGAATTTT
Statistics
Matches: 405, Mismatches: 6, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
404 77 0.19
405 328 0.81
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (404 bp):
GGCCTACATTATTTTTGTTCTTGAAAACGAGAAAAGAATGTCTTTACATCCAAAATAAGGATCAT
GAAATCAAGCCCAAACCCCAAAATCAATTGGAAACTGATTTCACCATAAAATATCCTAATCACTC
GGAGTCAATGAATGCATCGTTTAGACGCCAATGCTCATGCAAATACTAACATACATCATATGCAC
ATATACCATACATGCTTTTCACATCAGAACATACTAACAAATCATATGACAGATCATATACAAAT
TTCATTTTAAACATACTTGCAATTGTAACACATACCTTATCCTTATTACGTACATTCACAAAATC
TCATATTTCATATTTAGAATCATATTTAAGCGAAACCGACCCCCATGAAAGGTCTAATTATGAAT
TTCATAGCCTAACA
Found at i:1733545 original size:17 final size:17
Alignment explanation
Indices: 1733525--1733559 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1733515 TGACACATGG
*
1733525 CTGTGTGCCACACGCGA
1 CTGTGTGCCACACACGA
*
1733542 CTGTGTGTCACACACGA
1 CTGTGTGCCACACACGA
1733559 C
1 C
1733560 CTGGCACACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.34, G:0.26, T:0.20
Consensus pattern (17 bp):
CTGTGTGCCACACACGA
Found at i:1735827 original size:14 final size:16
Alignment explanation
Indices: 1735808--1735839 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
1735798 GAAGTGAATA
1735808 TTGCAAA-TA-ATTTT
1 TTGCAAATTATATTTT
1735822 TTGCAAATTATATTTT
1 TTGCAAATTATATTTT
1735838 TT
1 TT
1735840 TTATTAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 2 0.12
16 7 0.44
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.56
Consensus pattern (16 bp):
TTGCAAATTATATTTT
Found at i:1743537 original size:2 final size:2
Alignment explanation
Indices: 1743532--1743562 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1743522 AGTCAGAAAC
1743532 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1743563 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1743640 original size:2 final size:2
Alignment explanation
Indices: 1743635--1743659 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1743625 AGTATATATA
1743635 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
1743660 ATCAATATAT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1743849 original size:8 final size:8
Alignment explanation
Indices: 1743836--1743965 Score: 152
Period size: 8 Copynumber: 15.2 Consensus size: 8
1743826 AAACTAACAT
1743836 TATATGTA
1 TATATGTA
1743844 TATATGTA
1 TATATGTA
1743852 TATATGTA
1 TATATGTA
1743860 TATACATGTA
1 TAT--ATGTA
*
1743870 TACATGTA
1 TATATGTA
1743878 TATATGTA
1 TATATGTA
1743886 TATACATGTA
1 TAT--ATGTA
*
1743896 TACATGTA
1 TATATGTA
1743904 TATATGTA
1 TATATGTA
1743912 TATACATGTA
1 TAT--ATGTA
*
1743922 TACATGTA
1 TATATGTA
1743930 TATATGTATA
1 TATATG--TA
1743940 TATATGTA
1 TATATGTA
*
1743948 TATATGCA
1 TATATGTA
1743956 TATATGTA
1 TATATGTA
1743964 TA
1 TA
1743966 AAAAATATGT
Statistics
Matches: 106, Mismatches: 8, Indels: 16
0.82 0.06 0.12
Matches are distributed among these distances:
8 77 0.73
10 29 0.27
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (8 bp):
TATATGTA
Found at i:1743868 original size:18 final size:17
Alignment explanation
Indices: 1743836--1743965 Score: 135
Period size: 18 Copynumber: 7.6 Consensus size: 17
1743826 AAACTAACAT
1743836 TATATGTATAT-ATGTA
1 TATATGTATATAATGTA
1743852 TATATGTATATACATGTA
1 TATATGTATATA-ATGTA
*
1743870 TACATGTATAT-ATGTA
1 TATATGTATATAATGTA
*
1743886 TATACATGTATA-CATGTA
1 TAT--ATGTATATAATGTA
1743904 TATATGTATATACATGTA
1 TATATGTATATA-ATGTA
*
1743922 TACATGTATAT-ATGTATA
1 TATATGTATATAATG--TA
*
1743940 TATATGTATAT-ATGCA
1 TATATGTATATAATGTA
1743956 TATATGTATA
1 TATATGTATA
1743966 AAAAATATGT
Statistics
Matches: 99, Mismatches: 6, Indels: 18
0.80 0.05 0.15
Matches are distributed among these distances:
16 39 0.39
18 60 0.61
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (17 bp):
TATATGTATATAATGTA
Found at i:1743870 original size:26 final size:26
Alignment explanation
Indices: 1743839--1743965 Score: 218
Period size: 26 Copynumber: 4.9 Consensus size: 26
1743829 CTAACATTAT
*
1743839 ATGTATATATGTATATATGTATATAC
1 ATGTATACATGTATATATGTATATAC
1743865 ATGTATACATGTATATATGTATATAC
1 ATGTATACATGTATATATGTATATAC
1743891 ATGTATACATGTATATATGTATATAC
1 ATGTATACATGTATATATGTATATAC
*
1743917 ATGTATACATGTATATATGTATATAT
1 ATGTATACATGTATATATGTATATAC
* *
1743943 ATGTATATATGCATATATGTATA
1 ATGTATACATGTATATATGTATA
1743966 AAAAATATGT
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 97 1.00
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.44
Consensus pattern (26 bp):
ATGTATACATGTATATATGTATATAC
Found at i:1752694 original size:21 final size:21
Alignment explanation
Indices: 1752637--1752686 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1752627 AATAGTGTAG
1752637 ACTTCTACCGATACAAGTGAC
1 ACTTCTACCGATACAAGTGAC
**
1752658 AGGTCTACCGATACAAGTGAC
1 ACTTCTACCGATACAAGTGAC
*
1752679 TCTTCTAC
1 ACTTCTAC
1752687 TGAAACAAAT
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:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTGAC
Found at i:1753527 original size:52 final size:52
Alignment explanation
Indices: 1753446--1753788 Score: 519
Period size: 52 Copynumber: 6.6 Consensus size: 52
1753436 ATTTCAATTA
* * *
1753446 ATACTCACGATGACACATAGTCATCGGACCTCTTAATTCGTAAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGAATCAT
* * * *
1753498 ATACTCACGATGATACATAATCATTGGACCTCATAATCCGTAAA-GAATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGAA-TCAT
* **
1753550 ATACTCACGATGACACATAGTCATCGAACCTCATAATCTGTAAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGAATCAT
1753602 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAA-GAATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGAA-TCAT
1753654 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGAATCAT
* * * * *
1753706 GTACTCATGATGACACATAGTCATCGGAGCTCATAATCCATAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGAATCAT
1753758 ATACTCACGATGACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
1753789 TTTTCATTTA
Statistics
Matches: 266, Mismatches: 21, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
51 6 0.02
52 254 0.95
53 6 0.02
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGAATCAT
Found at i:1760223 original size:41 final size:41
Alignment explanation
Indices: 1760166--1760261 Score: 142
Period size: 41 Copynumber: 2.3 Consensus size: 41
1760156 GAATTTTATT
1760166 TTAACAAGAATTCTAGTCA-CTCAATTCTAACAATC-CCTAAC
1 TTAACAAGAATTCTAGTCATC-CAATTCTAACAATCTCC-AAC
*
1760207 TTAACAAGAATTCTAGTCATCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCATCCAATTCTAACAATCTCCAAC
*
1760248 TTGACAAGAATTCT
1 TTAACAAGAATTCT
1760262 CTACGAACAA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
41 48 0.94
42 3 0.06
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.30
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCATCCAATTCTAACAATCTCCAAC
Found at i:1764571 original size:28 final size:28
Alignment explanation
Indices: 1764536--1764589 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
1764526 TGAAACACCT
*
1764536 TATTCTAATTAAAATAAAATAGAAGACC
1 TATTCTAATTAAAATAAAATAAAAGACC
*
1764564 TATTCTAATTGAAATAAAATAAAAGA
1 TATTCTAATTAAAATAAAATAAAAGA
1764590 AGTCTAGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (28 bp):
TATTCTAATTAAAATAAAATAAAAGACC
Found at i:1764762 original size:38 final size:37
Alignment explanation
Indices: 1764700--1764785 Score: 163
Period size: 38 Copynumber: 2.3 Consensus size: 37
1764690 TGAATGATGG
1764700 TGGTGGTGGTGCAGTGTGAAGAAGAAGAAGACGACGA
1 TGGTGGTGGTGCAGTGTGAAGAAGAAGAAGACGACGA
1764737 TGGTGGTGGTGCAAGTGTGAAGAAGAAGAAGACGACGA
1 TGGTGGTGGTGC-AGTGTGAAGAAGAAGAAGACGACGA
1764775 TGGTGGTGGTG
1 TGGTGGTGGTG
1764786 AACTTGAATG
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
37 12 0.25
38 36 0.75
ACGTcount: A:0.29, C:0.07, G:0.45, T:0.19
Consensus pattern (37 bp):
TGGTGGTGGTGCAGTGTGAAGAAGAAGAAGACGACGA
Found at i:1769956 original size:17 final size:17
Alignment explanation
Indices: 1769934--1770033 Score: 101
Period size: 17 Copynumber: 5.9 Consensus size: 17
1769924 AAATTTTAAT
* *
1769934 TTTTAATTTTTAATTTA
1 TTTTAAATTTAAATTTA
* *
1769951 TTTTAAGTTTGAATTTA
1 TTTTAAATTTAAATTTA
* *
1769968 TTTTAAATTTAAACTCA
1 TTTTAAATTTAAATTTA
* * *
1769985 TTTTGAGTTTGAATTTA
1 TTTTAAATTTAAATTTA
*
1770002 CTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
*
1770019 TTTTAAATTGAAATT
1 TTTTAAATTTAAATT
1770034 AATTAAAAAG
Statistics
Matches: 66, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 66 1.00
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:1769972 original size:34 final size:34
Alignment explanation
Indices: 1769934--1770024 Score: 128
Period size: 34 Copynumber: 2.7 Consensus size: 34
1769924 AAATTTTAAT
* *
1769934 TTTTAATTTTTAATTTATTTTAAGTTTGAATTTA
1 TTTTAAATTTAAATTTATTTTAAGTTTGAATTTA
* * *
1769968 TTTTAAATTTAAACTCATTTTGAGTTTGAATTTA
1 TTTTAAATTTAAATTTATTTTAAGTTTGAATTTA
*
1770002 CTTTAAATTTAAATTTATTTTAA
1 TTTTAAATTTAAATTTATTTTAA
1770025 ATTGAAATTA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.58
Consensus pattern (34 bp):
TTTTAAATTTAAATTTATTTTAAGTTTGAATTTA
Found at i:1770645 original size:21 final size:20
Alignment explanation
Indices: 1770630--1770689 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 20
1770620 TTAATAGATG
1770630 GTAATAAATAAATAATAA-A
1 GTAATAAATAAATAATAATA
*
1770649 GTATATTAATAAATAA-ATATA
1 GTA-ATAAATAAATAATA-ATA
1770670 GTAATAATAATAAATAATAA
1 GTAAT-A-AATAAATAATAA
1770690 AAAGAAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
19 4 0.12
20 14 0.42
21 4 0.12
22 10 0.30
23 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (20 bp):
GTAATAAATAAATAATAATA
Found at i:1770669 original size:16 final size:17
Alignment explanation
Indices: 1770643--1770676 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1770633 ATAAATAAAT
*
1770643 AATAAAGTATATTAATA
1 AATAAAGTATAGTAATA
1770660 AATAAA-TATAGTAATA
1 AATAAAGTATAGTAATA
1770676 A
1 A
1770677 TAATAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (17 bp):
AATAAAGTATAGTAATA
Found at i:1774788 original size:23 final size:23
Alignment explanation
Indices: 1774762--1774971 Score: 202
Period size: 23 Copynumber: 9.3 Consensus size: 23
1774752 ACACTAATGC
1774762 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
* *
1774785 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
*
1774808 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
* *
1774831 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
* * **
1774854 GCTCTCTGTTTAGCACGTCT-CAT
1 GCTCTCTGATTAGCAC-TTTGTGT
* *
1774877 GCTCTCTGTTATTAGCACATCGTGT
1 GCTCTCTG--ATTAGCACTTTGTGT
1774902 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
*
1774925 G--CTC-----AGTACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
* * *
1774941 ACTCTCTGTTTAGTACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
1774964 GCTCTCTG
1 GCTCTCTG
1774972 TTACCCAGCA
Statistics
Matches: 154, Mismatches: 22, Indels: 22
0.78 0.11 0.11
Matches are distributed among these distances:
16 11 0.07
18 3 0.02
21 3 0.02
23 119 0.77
24 2 0.01
25 16 0.10
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTTTGTGT
Found at i:1774829 original size:46 final size:46
Alignment explanation
Indices: 1774762--1774928 Score: 230
Period size: 46 Copynumber: 3.6 Consensus size: 46
1774752 ACACTAATGC
1774762 GCTCTCTGATTAGCACTTTGTGTGCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTTTGTGTGCTCTCTGTTTAGCACTGTGTGT
*
1774808 GCTCTCTGATTAGTACTTTGTGTGCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTTTGTGTGCTCTCTGTTTAGCACTGTGTGT
* * ** *
1774854 GCTCTCTGTTTAGCACGTCT-CATGCTCTCTGTTATTAGCACAT-CGTGT
1 GCTCTCTGATTAGCAC-TTTGTGTGCTCTCTG-T-TTAGCAC-TGTGTGT
1774902 GCTCTCTGATTAGCACTTTGTGTGCTC
1 GCTCTCTGATTAGCACTTTGTGTGCTC
1774929 AGTACTTTGT
Statistics
Matches: 105, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
46 68 0.65
47 5 0.05
48 31 0.30
49 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTTTGTGTGCTCTCTGTTTAGCACTGTGTGT
Found at i:1774880 original size:69 final size:70
Alignment explanation
Indices: 1774762--1774928 Score: 239
Period size: 69 Copynumber: 2.4 Consensus size: 70
1774752 ACACTAATGC
* * * *
1774762 GCTCTCTGATTAGCACTTTGTGTGCTCTCTGTTTAGCACTGTGTGTGCTCTCTG-ATTAGTACTT
1 GCTCTCTGATTAGCACTTTGTGTGCTCTCTGTTTAGCACTGTCTATGCTCTCTGTATTAGCACAT
*
1774826 TGTGT
66 CGTGT
* *
1774831 GCTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTTAGCAC-GTCTCATGCTCTCTGTTATTAGCAC
1 GCTCTCTGATTAGCACTTTGTGTGCTCTCTGTTTAGCACTGTCT-ATGCTCTCTG-TATTAGCAC
1774895 ATCGTGT
64 ATCGTGT
1774902 GCTCTCTGATTAGCACTTTGTGTGCTC
1 GCTCTCTGATTAGCACTTTGTGTGCTC
1774929 AGTACTTTGT
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
68 3 0.03
69 46 0.53
71 37 0.43
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (70 bp):
GCTCTCTGATTAGCACTTTGTGTGCTCTCTGTTTAGCACTGTCTATGCTCTCTGTATTAGCACAT
CGTGT
Found at i:1785864 original size:3 final size:3
Alignment explanation
Indices: 1785856--1785882 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1785846 ATATAACTAC
1785856 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1785883 TTGGTGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1802113 original size:26 final size:27
Alignment explanation
Indices: 1802079--1802129 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
1802069 TTAGAAAAGG
1802079 AAAATGAGAAAA-AGAAAGAAAAAAAAT
1 AAAATGAGAAAAGA-AAAGAAAAAAAAT
*
1802106 AAAA-GAGAAATGAAAAGAAAAAAA
1 AAAATGAGAAAAGAAAAGAAAAAAA
1802130 TGTTTGCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (27 bp):
AAAATGAGAAAAGAAAAGAAAAAAAAT
Found at i:1802129 original size:20 final size:19
Alignment explanation
Indices: 1802087--1802126 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 19
1802077 GGAAAATGAG
1802087 AAAAAGAAAGAAAAAAAAT
1 AAAAAGAAAGAAAAAAAAT
1802106 AAAAGAGAAATGAAAAGAAAA
1 AAAA-AGAAA-GAAAA-AAAA
1802127 AAATGTTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 5 0.28
21 5 0.28
22 4 0.22
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (19 bp):
AAAAAGAAAGAAAAAAAAT
Found at i:1807713 original size:108 final size:110
Alignment explanation
Indices: 1807503--1807704 Score: 266
Period size: 108 Copynumber: 1.9 Consensus size: 110
1807493 TAAATAACAC
* ** * * *
1807503 TTATTGATTTTAAAATAGGATGTTCAATTACTTAACTTTAAAGAAAAATTATACTCAGTACGTTA
1 TTATCGATTTTAAAATAGGATACTCAATTACTTAACTTTAAAGAAAAACTATACCCAATACGTTA
* **
1807568 GGGTACAATTTTTTGATTCTCCTAAAATAATAGAACATCGAGCAT
66 GGGCACAATTTTTAAATTCTCCTAAAATAATAGAACATCGAGCAT
* * *
1807613 TTATCGATTTT-AAATAGGATACTCAATTATTTAAGTTTAAA-AAAAACTATACCCAATATGTTA
1 TTATCGATTTTAAAATAGGATACTCAATTACTTAACTTTAAAGAAAAACTATACCCAATACGTTA
1807676 GGGCACAATTTTTCAAATTC-CCTAAAATA
66 GGGCACAATTTTT-AAATTCTCCTAAAATA
1807705 GAATAACATT
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
108 39 0.49
109 30 0.38
110 10 0.13
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.37
Consensus pattern (110 bp):
TTATCGATTTTAAAATAGGATACTCAATTACTTAACTTTAAAGAAAAACTATACCCAATACGTTA
GGGCACAATTTTTAAATTCTCCTAAAATAATAGAACATCGAGCAT
Found at i:1808012 original size:25 final size:28
Alignment explanation
Indices: 1807953--1808017 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 28
1807943 TTAAAAACAT
*
1807953 AATAAAAAGGTTAATTTTTTTTAAATAG
1 AATAAAAAGATTAATTTTTTTTAAATAG
*
1807981 AACAAAAAGATTAA-TTTTTTT-AA-AG
1 AATAAAAAGATTAATTTTTTTTAAATAG
*
1808006 AATAAAATGATT
1 AATAAAAAGATT
1808018 CTCCTGTCTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 12 0.36
26 2 0.06
27 7 0.21
28 12 0.36
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (28 bp):
AATAAAAAGATTAATTTTTTTTAAATAG
Found at i:1809635 original size:7 final size:7
Alignment explanation
Indices: 1809623--1809691 Score: 79
Period size: 7 Copynumber: 10.1 Consensus size: 7
1809613 TCTTGACCTC
1809623 TCTTTTT
1 TCTTTTT
1809630 TC-TTTT
1 TCTTTTT
*
1809636 TCTTTCT
1 TCTTTTT
1809643 TCTTTTT
1 TCTTTTT
* *
1809650 CCATTTT
1 TCTTTTT
* *
1809657 CCATTTT
1 TCTTTTT
1809664 TCTTTTT
1 TCTTTTT
1809671 TCTTTTT
1 TCTTTTT
1809678 T-TTTTT
1 TCTTTTT
1809684 TCTTTTT
1 TCTTTTT
1809691 T
1 T
1809692 TGGTGAAATA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
6 12 0.22
7 42 0.78
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (7 bp):
TCTTTTT
Found at i:1809692 original size:13 final size:13
Alignment explanation
Indices: 1809623--1809690 Score: 82
Period size: 13 Copynumber: 5.1 Consensus size: 13
1809613 TCTTGACCTC
1809623 TCTTTTTTCTTTT
1 TCTTTTTTCTTTT
*
1809636 TCTTTCTTCTTTT
1 TCTTTTTTCTTTT
* *
1809649 TCCATTTTCCATTTT
1 T-CTTTTTTC-TTTT
1809664 TCTTTTTTCTTTT
1 TCTTTTTTCTTTT
*
1809677 TTTTTTTTCTTTT
1 TCTTTTTTCTTTT
1809690 T
1 T
1809691 TTGGTGAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
13 30 0.65
14 11 0.24
15 5 0.11
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (13 bp):
TCTTTTTTCTTTT
Found at i:1812823 original size:21 final size:21
Alignment explanation
Indices: 1812780--1812827 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1812770 CTTGGGAAAT
* *
1812780 TTCTACTGATACAAGTGTAAC
1 TTCTACTGAAACAAGTATAAC
1812801 TTCTACTGAAACAAGTCAT-AC
1 TTCTACTGAAACAAGT-ATAAC
1812822 TTCTAC
1 TTCTAC
1812828 CGGTACTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (21 bp):
TTCTACTGAAACAAGTATAAC
Found at i:1816548 original size:26 final size:26
Alignment explanation
Indices: 1816508--1816630 Score: 104
Period size: 26 Copynumber: 4.7 Consensus size: 26
1816498 ATAAATAATA
*
1816508 AAAAATAGAACAAAATGATTAAATTTT
1 AAAAA-AGAATAAAATGATTAAATTTT
* *
1816535 AAAAAAGAATAAAATGATTTAA-TTA
1 AAAAAAGAATAAAATGATTAAATTTT
* * * *
1816560 AAAAAATAATAAAAAGGTTAATTTTT
1 AAAAAAGAATAAAATGATTAAATTTT
* * * * *
1816586 TAAATAGAACAAAAAGATTAATTTTT
1 AAAAAAGAATAAAATGATTAAATTTT
**
1816612 TTAAAAGAATAAAATGATT
1 AAAAAAGAATAAAATGATT
1816631 TAAAAAAATA
Statistics
Matches: 77, Mismatches: 18, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
25 19 0.25
26 53 0.69
27 5 0.06
ACGTcount: A:0.59, C:0.02, G:0.08, T:0.32
Consensus pattern (26 bp):
AAAAAAGAATAAAATGATTAAATTTT
Found at i:1816570 original size:25 final size:26
Alignment explanation
Indices: 1816506--1816664 Score: 94
Period size: 26 Copynumber: 6.2 Consensus size: 26
1816496 AAATAAATAA
*
1816506 TAAAAAATAGAACAAAATGATTAAATT
1 TAAAAAA-AGAATAAAATGATTAAATT
* *
1816533 TTAAAAAAGAATAAAATGATTTAA-T
1 TAAAAAAAGAATAAAATGATTAAATT
* * * *
1816558 TAAAAAAATAATAAAAAGGTTAATTT
1 TAAAAAAAGAATAAAATGATTAAATT
** * * * *
1816584 TTTAAATAGAACAAAAAGATTAATTT
1 TAAAAAAAGAATAAAATGATTAAATT
*** *
1816610 TTTTAAAAGAATAAAATGATTTAA--
1 TAAAAAAAGAATAAAATGATTAAATT
* *
1816634 -AAAAATATAATAAAA-GAGTTAAATT
1 TAAAAAAAGAATAAAATGA-TTAAATT
1816659 TAAAAA
1 TAAAAA
1816665 GAAAAACAAA
Statistics
Matches: 100, Mismatches: 27, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
22 2 0.02
23 14 0.14
25 19 0.19
26 59 0.59
27 6 0.06
ACGTcount: A:0.60, C:0.01, G:0.08, T:0.31
Consensus pattern (26 bp):
TAAAAAAAGAATAAAATGATTAAATT
Found at i:1816580 original size:24 final size:25
Alignment explanation
Indices: 1816535--1816582 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1816525 ATTAAATTTT
* *
1816535 AAAAAAGAATAAAATGATTTAATTA
1 AAAAAAGAATAAAAAGAGTTAATTA
*
1816560 AAAAAATAATAAAAAG-GTTAATT
1 AAAAAAGAATAAAAAGAGTTAATT
1816583 TTTTAAATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (25 bp):
AAAAAAGAATAAAAAGAGTTAATTA
Found at i:1828065 original size:21 final size:22
Alignment explanation
Indices: 1828032--1828077 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
1828022 TACCGGTAGT
*
1828032 CTTTAATGATTTACCGATACAA
1 CTTTAATGATTTACCGAAACAA
*
1828054 CTTTATTG-TTTACCGAAACAA
1 CTTTAATGATTTACCGAAACAA
1828075 CTT
1 CTT
1828078 GACCATCTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.39
Consensus pattern (22 bp):
CTTTAATGATTTACCGAAACAA
Found at i:1831930 original size:30 final size:32
Alignment explanation
Indices: 1831876--1831934 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
1831866 AAATTATGAG
*
1831876 ATTTCACGATTTGGGAATATAAGGGATTAGGC
1 ATTTCACGATTTGAGAATATAAGGGATTAGGC
*
1831908 ATTTCATGATTTGAG-A-ATAAGGGATTA
1 ATTTCACGATTTGAGAATATAAGGGATTA
1831935 AGTAGAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 11 0.44
31 1 0.04
32 13 0.52
ACGTcount: A:0.34, C:0.07, G:0.25, T:0.34
Consensus pattern (32 bp):
ATTTCACGATTTGAGAATATAAGGGATTAGGC
Found at i:1835955 original size:29 final size:29
Alignment explanation
Indices: 1835899--1835956 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1835889 ATTCAATTCT
*** *
1835899 CAATAAAAAGTAATAGTTTTTTTATAAAA
1 CAATAAAAAGTAATAGTTAAATGATAAAA
*
1835928 CAATAAAAAGTAATAGTTAAATGCTAAAA
1 CAATAAAAAGTAATAGTTAAATGATAAAA
1835957 TTCAGACTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.31
Consensus pattern (29 bp):
CAATAAAAAGTAATAGTTAAATGATAAAA
Found at i:1836041 original size:20 final size:20
Alignment explanation
Indices: 1836007--1836044 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1835997 AAGAAAATGC
1836007 TTAAATAAATATTAAATATT
1 TTAAATAAATATTAAATATT
1836027 TTAAA-AAATACTTAAATA
1 TTAAATAAATA-TTAAATA
1836045 AAAACTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
TTAAATAAATATTAAATATT
Found at i:1843816 original size:21 final size:22
Alignment explanation
Indices: 1843770--1843819 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1843760 TAAAATTTTT
* * *
1843770 GGGTTTAGGGTTTATGGTTTTA
1 GGGTTTAAGGTTTATGGGTATA
1843792 -GGTTTAAGGTTT-TGGGTATA
1 GGGTTTAAGGTTTATGGGTATA
1843812 GGGTTTAA
1 GGGTTTAA
1843820 TTATGTGGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.18, C:0.00, G:0.36, T:0.46
Consensus pattern (22 bp):
GGGTTTAAGGTTTATGGGTATA
Found at i:1843888 original size:6 final size:6
Alignment explanation
Indices: 1843877--1843992 Score: 58
Period size: 6 Copynumber: 18.3 Consensus size: 6
1843867 CCTAAACTTC
* * * *
1843877 AAACAT AAACAT AAGCAT AAATAT AATTA-ATT AAATAC AAACAT AAACAT
1 AAACAT AAACAT AAACAT AAACAT AA--ACA-T AAACAT AAACAT AAACAT
* * * *
1843927 AAACAT AATTA-ATT AAATAC AAACAT AAACAT AATTA-ATT AAATAC
1 AAACAT AA--ACA-T AAACAT AAACAT AAACAT AA--ACA-T AAACAT
1843973 AAACAT AAACAT AAACAT AA
1 AAACAT AAACAT AAACAT AA
1843993 TTAATTCCAA
Statistics
Matches: 86, Mismatches: 12, Indels: 24
0.70 0.10 0.20
Matches are distributed among these distances:
6 68 0.79
7 6 0.07
8 12 0.14
ACGTcount: A:0.63, C:0.12, G:0.01, T:0.24
Consensus pattern (6 bp):
AAACAT
Found at i:1843911 original size:26 final size:26
Alignment explanation
Indices: 1843904--1843986 Score: 103
Period size: 26 Copynumber: 3.1 Consensus size: 26
1843894 TAAATATAAT
*
1843904 TAATTAAATACAAACATAAACATAAACA
1 TAATTAATTA-AA-CATAAACATAAACA
* *
1843932 TAATTAATTAAATACAAACATAAACA
1 TAATTAATTAAACATAAACATAAACA
* *
1843958 TAATTAATTAAATACAAACATAAACA
1 TAATTAATTAAACATAAACATAAACA
1843984 TAA
1 TAA
1843987 ACATAATTAA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
26 41 0.79
27 2 0.04
28 9 0.17
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.25
Consensus pattern (26 bp):
TAATTAATTAAACATAAACATAAACA
Found at i:1843919 original size:32 final size:32
Alignment explanation
Indices: 1843883--1843998 Score: 172
Period size: 32 Copynumber: 3.8 Consensus size: 32
1843873 CTTCAAACAT
* *
1843883 AAACATAAGCATAAATATAATTAATTAAATAC
1 AAACATAAACATAAACATAATTAATTAAATAC
1843915 AAACATAAACATAAACATAATTAATTAAAT--
1 AAACATAAACATAAACATAATTAATTAAATAC
1843945 --AC--AAACATAAACATAATTAATTAAATAC
1 AAACATAAACATAAACATAATTAATTAAATAC
1843973 AAACATAAACATAAACATAATTAATT
1 AAACATAAACATAAACATAATTAATT
1843999 CCAAATTCAT
Statistics
Matches: 76, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
26 24 0.32
28 2 0.03
30 2 0.03
32 48 0.63
ACGTcount: A:0.61, C:0.11, G:0.01, T:0.27
Consensus pattern (32 bp):
AAACATAAACATAAACATAATTAATTAAATAC
Found at i:1846666 original size:14 final size:14
Alignment explanation
Indices: 1846647--1846683 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
1846637 AAATTACCTT
1846647 TAAACACATTTAAC
1 TAAACACATTTAAC
1846661 TAAACACATTTAAC
1 TAAACACATTTAAC
1846675 TAAACACAT
1 TAAACACAT
1846684 AAACATACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (14 bp):
TAAACACATTTAAC
Found at i:1847099 original size:28 final size:30
Alignment explanation
Indices: 1847033--1847103 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
1847023 ACAACATAAT
*
1847033 ACAATATTT-AATAAAAAATTAAATTAACAA
1 ACAATATTTAAAAAAAAAATTAAA-TAACAA
*
1847063 ACAATATTTAAAAAAAAAATTAAA-ATCAA
1 ACAATATTTAAAAAAAAAATTAAATAACAA
*
1847092 CCAA-ATTTAAAA
1 ACAATATTTAAAA
1847104 TTTAAATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 8 0.22
29 7 0.19
30 9 0.24
31 13 0.35
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (30 bp):
ACAATATTTAAAAAAAAAATTAAATAACAA
Found at i:1847475 original size:27 final size:27
Alignment explanation
Indices: 1847444--1847496 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1847434 AGTAGCTTTG
*
1847444 TGGTGCAGTCTG-TCAAGTAGGCACCAT
1 TGGTGCAGCCTGCT-AAGTAGGCACCAT
*
1847471 TGGTGCCGCCTGCTAAGTAGGCACCA
1 TGGTGCAGCCTGCTAAGTAGGCACCA
1847497 CTCCTTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.21, C:0.26, G:0.30, T:0.23
Consensus pattern (27 bp):
TGGTGCAGCCTGCTAAGTAGGCACCAT
Found at i:1847565 original size:3 final size:3
Alignment explanation
Indices: 1847559--1847592 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1847549 TTTTTTATTT
1847559 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1847593 TGTCAGATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1860713 original size:28 final size:27
Alignment explanation
Indices: 1860660--1860713 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 27
1860650 TTCAATTTCG
** *
1860660 AAATTGAGTAAATTAATCTTTCTCAAA
1 AAATTGAGTAAATTAATCCCTATCAAA
*
1860687 AAATTAGAGTAATTTAATCCCTATCAA
1 AAATT-GAGTAAATTAATCCCTATCAA
1860714 TTTTAAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.35
Consensus pattern (27 bp):
AAATTGAGTAAATTAATCCCTATCAAA
Found at i:1862044 original size:21 final size:21
Alignment explanation
Indices: 1862017--1862067 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
1862007 GGATTATGTA
1862017 ATTTGGATTTATAAACTTTAT
1 ATTTGGATTTATAAACTTTAT
* *
1862038 GTTTGGATTTCTAAACTTTAT
1 ATTTGGATTTATAAACTTTAT
1862059 ATTTGGATT
1 ATTTGGATT
1862068 ATGCTATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.06, G:0.14, T:0.53
Consensus pattern (21 bp):
ATTTGGATTTATAAACTTTAT
Found at i:1866546 original size:20 final size:21
Alignment explanation
Indices: 1866523--1866567 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1866513 AATAGATTTA
*
1866523 ATAA-TAAATTTTATATTTTT
1 ATAATTAAATGTTATATTTTT
*
1866543 ATAATTAAATGTTATTTTTTT
1 ATAATTAAATGTTATATTTTT
1866564 ATAA
1 ATAA
1866568 ACATTAATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
ATAATTAAATGTTATATTTTT
Found at i:1867909 original size:21 final size:22
Alignment explanation
Indices: 1867883--1867932 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
1867873 TTTTTAATTA
1867883 TTTTATTCA-AAATT-GATAAAT
1 TTTTATT-ATAAATTAGATAAAT
*
1867904 TTTTATTATAAATTAGATCAAT
1 TTTTATTATAAATTAGATAAAT
*
1867926 TCTTATT
1 TTTTATT
1867933 TAATTACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 12 0.48
22 12 0.48
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (22 bp):
TTTTATTATAAATTAGATAAAT
Found at i:1867931 original size:22 final size:21
Alignment explanation
Indices: 1867892--1867932 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1867882 ATTTTATTCA
*
1867892 AAATTGATAAATTTTTATTAT
1 AAATTGATAAATTCTTATTAT
*
1867913 AAATTAGATCAATTCTTATT
1 AAATT-GATAAATTCTTATT
1867933 TAATTACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (21 bp):
AAATTGATAAATTCTTATTAT
Found at i:1869568 original size:42 final size:42
Alignment explanation
Indices: 1869521--1869604 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
1869511 AAAAAGAGTT
* * *
1869521 GTTTATGAGTGTTATTTAGGAATAAAATTATATTTGGGTTTA
1 GTTTATGAGTATTATTTAAGAATAAAATTATATTTGAGTTTA
* *
1869563 GTTTATGAGTATTTTTTAAGAATGAAATTATATTTGAGTTTA
1 GTTTATGAGTATTATTTAAGAATAAAATTATATTTGAGTTTA
1869605 AAAATATTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (42 bp):
GTTTATGAGTATTATTTAAGAATAAAATTATATTTGAGTTTA
Found at i:1870444 original size:16 final size:16
Alignment explanation
Indices: 1870423--1870464 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
1870413 GAAATGCATA
1870423 AAAGCGCTTTCAGCTG
1 AAAGCGCTTTCAGCTG
1870439 AAAGCGCTTTCAGCTG
1 AAAGCGCTTTCAGCTG
1870455 AAAGCGCTTT
1 AAAGCGCTTT
1870465 TCGCGTGGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (16 bp):
AAAGCGCTTTCAGCTG
Found at i:1870664 original size:30 final size:30
Alignment explanation
Indices: 1870621--1870701 Score: 108
Period size: 30 Copynumber: 2.6 Consensus size: 30
1870611 CTACTCATTT
*
1870621 TCTCACACAATTCTCTCAAATTCTCAAATCGC
1 TCTCA-AC-ATTCTCTCAAATTCTCAAATCAC
*
1870653 TCTCAACATTCTCTCAAAATCTCAAATCAC
1 TCTCAACATTCTCTCAAATTCTCAAATCAC
* *
1870683 TCTCAAAATTCTCTTAAAT
1 TCTCAACATTCTCTCAAAT
1870702 ATTTTTTTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
30 37 0.84
31 2 0.05
32 5 0.11
ACGTcount: A:0.35, C:0.31, G:0.01, T:0.33
Consensus pattern (30 bp):
TCTCAACATTCTCTCAAATTCTCAAATCAC
Found at i:1871808 original size:17 final size:17
Alignment explanation
Indices: 1871775--1871808 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1871765 TCCCTGCCCC
**
1871775 TGCAAAATAATGTAAAA
1 TGCAAAATAATAAAAAA
1871792 TGCAAAATAATAAAAAA
1 TGCAAAATAATAAAAAA
1871809 ACCTAAATTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.09, T:0.21
Consensus pattern (17 bp):
TGCAAAATAATAAAAAA
Found at i:1871884 original size:19 final size:20
Alignment explanation
Indices: 1871846--1871884 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1871836 TTAGTTTCGA
*
1871846 GTTTATTTTTATCGTGATGT
1 GTTTATTTTTATCGTCATGT
*
1871866 GTTTATTTTTGTC-TCATGT
1 GTTTATTTTTATCGTCATGT
1871885 TACAATATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.13, C:0.08, G:0.18, T:0.62
Consensus pattern (20 bp):
GTTTATTTTTATCGTCATGT
Found at i:1873492 original size:38 final size:38
Alignment explanation
Indices: 1873437--1873528 Score: 96
Period size: 38 Copynumber: 2.4 Consensus size: 38
1873427 TGTTAGGCAT
* * *
1873437 TAAGCTCGATAACCACCGACAC-TAAGCCTACTAGACAC
1 TAAGCCCGATAAACACCGACACAT-ACCCTACTAGACAC
* * *
1873475 TAAGCCCGATAAACACCGGCACATACCCTGCTAGGCAC
1 TAAGCCCGATAAACACCGACACATACCCTACTAGACAC
* *
1873513 AAAGCCCAATAAACAC
1 TAAGCCCGATAAACAC
1873529 TGTACAATCA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
38 44 0.98
39 1 0.02
ACGTcount: A:0.38, C:0.35, G:0.14, T:0.13
Consensus pattern (38 bp):
TAAGCCCGATAAACACCGACACATACCCTACTAGACAC
Found at i:1878784 original size:30 final size:30
Alignment explanation
Indices: 1878741--1878821 Score: 108
Period size: 30 Copynumber: 2.6 Consensus size: 30
1878731 CTACTCATTT
*
1878741 TCTCACACAATTCTCTCAAATTCTCAAATCGC
1 TCTCA-AC-ATTCTCTCAAATTCTCAAATCAC
*
1878773 TCTCAACATTCTCTCAAAATCTCAAATCAC
1 TCTCAACATTCTCTCAAATTCTCAAATCAC
* *
1878803 TCTCAAAATTCTCTTAAAT
1 TCTCAACATTCTCTCAAAT
1878822 ATTTTTTTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
30 37 0.84
31 2 0.05
32 5 0.11
ACGTcount: A:0.35, C:0.31, G:0.01, T:0.33
Consensus pattern (30 bp):
TCTCAACATTCTCTCAAATTCTCAAATCAC
Found at i:1879928 original size:17 final size:17
Alignment explanation
Indices: 1879895--1879928 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1879885 TCCCTGCCCC
**
1879895 TGCAAAATAATGTAAAA
1 TGCAAAATAATAAAAAA
1879912 TGCAAAATAATAAAAAA
1 TGCAAAATAATAAAAAA
1879929 ACCTAAATTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.09, T:0.21
Consensus pattern (17 bp):
TGCAAAATAATAAAAAA
Found at i:1880004 original size:19 final size:20
Alignment explanation
Indices: 1879966--1880004 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1879956 TTAGTTTCGA
*
1879966 GTTTATTTTTATCGTGATGT
1 GTTTATTTTTATCGTCATGT
*
1879986 GTTTATTTTTGTC-TCATGT
1 GTTTATTTTTATCGTCATGT
1880005 TACAATATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.13, C:0.08, G:0.18, T:0.62
Consensus pattern (20 bp):
GTTTATTTTTATCGTCATGT
Found at i:1881612 original size:38 final size:38
Alignment explanation
Indices: 1881557--1881648 Score: 96
Period size: 38 Copynumber: 2.4 Consensus size: 38
1881547 TGTTAGGCAT
* * *
1881557 TAAGCTCGATAACCACCGACAC-TAAGCCTACTAGACAC
1 TAAGCCCGATAAACACCGACACAT-ACCCTACTAGACAC
* * *
1881595 TAAGCCCGATAAACACCGGCACATACCCTGCTAGGCAC
1 TAAGCCCGATAAACACCGACACATACCCTACTAGACAC
* *
1881633 AAAGCCCAATAAACAC
1 TAAGCCCGATAAACAC
1881649 TGTACAATCA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
38 44 0.98
39 1 0.02
ACGTcount: A:0.38, C:0.35, G:0.14, T:0.13
Consensus pattern (38 bp):
TAAGCCCGATAAACACCGACACATACCCTACTAGACAC
Found at i:1910736 original size:12 final size:12
Alignment explanation
Indices: 1910719--1910755 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1910709 AACATCTATG
1910719 AATTTTCTTTTA
1 AATTTTCTTTTA
1910731 AATTTTC-TTTA
1 AATTTTCTTTTA
1910742 AATTATT-TTTTA
1 AATT-TTCTTTTA
1910754 AA
1 AA
1910756 AAATATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 8 0.35
12 15 0.65
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (12 bp):
AATTTTCTTTTA
Found at i:1920375 original size:18 final size:19
Alignment explanation
Indices: 1920327--1920376 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
1920317 GAAGTCAATT
*
1920327 TTAAATATTATTTATATTA
1 TTAATTATTATTTATATTA
*
1920346 TTAATTA-GATTTATATCTA
1 TTAATTATTATTTATAT-TA
1920365 -T-ATTATTATTTA
1 TTAATTATTATTTA
1920377 CATATATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 4 0.15
18 14 0.54
19 8 0.31
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
TTAATTATTATTTATATTA
Found at i:1920393 original size:24 final size:24
Alignment explanation
Indices: 1920331--1920393 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
1920321 TCAATTTTAA
*
1920331 ATAT-TATTTATATTATTAATTAG
1 ATATATATTTATATTATTAATTAC
* * *
1920354 ATTTATATCTATATTATTATTTAC
1 ATATATATTTATATTATTAATTAC
1920378 ATATATAATTTA-ATTA
1 ATATAT-ATTTATATTA
1920394 ATGTAACGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
23 3 0.09
24 25 0.78
25 4 0.12
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.56
Consensus pattern (24 bp):
ATATATATTTATATTATTAATTAC
Found at i:1927091 original size:19 final size:20
Alignment explanation
Indices: 1927067--1927105 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1927057 TATATAATAT
*
1927067 ATAATATAT-TTTTATTAAA
1 ATAATATATAATTTATTAAA
1927086 ATAATATATAATTTATTAAA
1 ATAATATATAATTTATTAAA
1927106 GAACTAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATAATATATAATTTATTAAA
Found at i:1927092 original size:24 final size:24
Alignment explanation
Indices: 1927046--1927093 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1927036 TGTAATTGAG
*
1927046 ATATATTTGTATATATAATATATA
1 ATATATTTGTATATAAAATATATA
*
1927070 ATATATTTTTAT-TAAAATAATATA
1 ATATATTTGTATATAAAAT-ATATA
1927094 TAATTTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
ATATATTTGTATATAAAATATATA
Found at i:1927207 original size:2 final size:2
Alignment explanation
Indices: 1927202--1927232 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1927192 TCTATGTGTG
1927202 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1927233 TTGTGTGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1931579 original size:21 final size:21
Alignment explanation
Indices: 1931550--1931593 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1931540 AATGTGTCTA
* *
1931550 AATTATATTTTATATTTATTT
1 AATTATATTTTATAGTGATTT
*
1931571 AATTCTATTTTATAGTGATTT
1 AATTATATTTTATAGTGATTT
1931592 AA
1 AA
1931594 ATATGTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (21 bp):
AATTATATTTTATAGTGATTT
Found at i:1935740 original size:3 final size:3
Alignment explanation
Indices: 1935732--1935773 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1935722 CATCTGCAAC
1935732 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1935774 AGAACACGAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:1939545 original size:26 final size:24
Alignment explanation
Indices: 1939516--1939568 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 24
1939506 AATATATAAA
1939516 TTAACATTTTTATT-TTTTTTAGAAAT
1 TTAACATTTTT-TTATTTTTT-G-AAT
*
1939542 TTAATATTTTTTTATTTTTTGAAT
1 TTAACATTTTTTTATTTTTTGAAT
1939566 TTA
1 TTA
1939569 TATATATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 6 0.24
25 3 0.12
26 16 0.64
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (24 bp):
TTAACATTTTTTTATTTTTTGAAT
Found at i:1939551 original size:25 final size:26
Alignment explanation
Indices: 1939523--1939579 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 26
1939513 AAATTAACAT
1939523 TTTTATTT-TTTTTAGAAATTTA-ATA
1 TTTTATTTATTTTTAG-AATTTATATA
*
1939548 TTTT-TTTATTTTTTGAATTTATATA
1 TTTTATTTATTTTTAGAATTTATATA
1939573 TATTTAT
1 T-TTTAT
1939580 AAAATTTTCG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 9 0.33
25 14 0.52
26 3 0.11
27 1 0.04
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (26 bp):
TTTTATTTATTTTTAGAATTTATATA
Found at i:1939578 original size:23 final size:25
Alignment explanation
Indices: 1939526--1939579 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 25
1939516 TTAACATTTT
*
1939526 TATTT-TTTTTAGAAATTTAATATT
1 TATTTATTTTTAGAAATTTAATATA
* *
1939550 TTTTTATTTTTTG-AATTT-ATATA
1 TATTTATTTTTAGAAATTTAATATA
1939573 TATTTAT
1 TATTTAT
1939580 AAAATTTTCG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 10 0.40
24 9 0.36
25 6 0.24
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (25 bp):
TATTTATTTTTAGAAATTTAATATA
Found at i:1941050 original size:14 final size:15
Alignment explanation
Indices: 1941033--1941061 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1941023 TCATTGAATT
1941033 ATTTAAAATT-TAAA
1 ATTTAAAATTGTAAA
1941047 ATTTAAAATTGTAAA
1 ATTTAAAATTGTAAA
1941062 TTAAATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
ATTTAAAATTGTAAA
Found at i:1942818 original size:19 final size:19
Alignment explanation
Indices: 1942787--1942832 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1942777 AAATATTTAT
1942787 TAATAATATATTTATAATTA
1 TAATAA-ATATTTATAATTA
*
1942807 TAATAAATATTTATTATTA
1 TAATAAATATTTATAATTA
*
1942826 AAATAAA
1 TAATAAA
1942833 ATTGAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TAATAAATATTTATAATTA
Found at i:1948301 original size:17 final size:18
Alignment explanation
Indices: 1948279--1948316 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1948269 CTTGACCTTC
*
1948279 AACCTTCCATCTTTTT-T
1 AACCTTCCATATTTTTGT
*
1948296 AACCTTTCATATTTTTGT
1 AACCTTCCATATTTTTGT
1948314 AAC
1 AAC
1948317 TACTTTTTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.24, C:0.24, G:0.03, T:0.50
Consensus pattern (18 bp):
AACCTTCCATATTTTTGT
Found at i:1950539 original size:23 final size:23
Alignment explanation
Indices: 1950513--1950557 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
1950503 AAATATCCTT
1950513 AAAATAATCAGAGTTTAACTGAAA
1 AAAATAATCA-AGTTTAACTGAAA
1950537 AAAGATAA-CAAGTTTAACTGA
1 AAA-ATAATCAAGTTTAACTGA
1950558 GAGAATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 11 0.55
24 5 0.25
25 4 0.20
ACGTcount: A:0.53, C:0.09, G:0.13, T:0.24
Consensus pattern (23 bp):
AAAATAATCAAGTTTAACTGAAA
Found at i:1951384 original size:23 final size:23
Alignment explanation
Indices: 1951341--1951385 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1951331 ATATATTCAA
*
1951341 ATTAAATTTTACAAATAATTTAT
1 ATTAAATTTTAAAAATAATTTAT
1951364 ATTAAATTTTTAAAAAT-ATTTA
1 ATTAAA-TTTTAAAAATAATTTA
1951386 AAATTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTAAATTTTAAAAATAATTTAT
Found at i:1952107 original size:6 final size:6
Alignment explanation
Indices: 1952096--1952120 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1952086 TATATTTTAA
1952096 ATAATT ATAATT ATAATT ATAATT A
1 ATAATT ATAATT ATAATT ATAATT A
1952121 AATATTATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATAATT
Found at i:1958468 original size:28 final size:28
Alignment explanation
Indices: 1958426--1958490 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 28
1958416 AAAATAAGAC
1958426 TTTTCGGATACTCGGGGGC-AAAATGGTAA
1 TTTT-GGATACTC-GGGGCAAAAATGGTAA
*
1958455 TTTTGGATTCTCGGGGCAAAAAATGGTAA
1 TTTTGGATACTCGGGGC-AAAAATGGTAA
1958484 TTTTGGA
1 TTTTGGA
1958491 AAATTTGAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
27 5 0.15
28 7 0.21
29 21 0.64
ACGTcount: A:0.28, C:0.11, G:0.29, T:0.32
Consensus pattern (28 bp):
TTTTGGATACTCGGGGCAAAAATGGTAA
Found at i:1958616 original size:59 final size:59
Alignment explanation
Indices: 1958553--1958790 Score: 331
Period size: 59 Copynumber: 4.0 Consensus size: 59
1958543 ATTTTAGAGG
*
1958553 TTTGAGGGT-AAAAAT-GGAATTTTTGAAAGTTTAGGGGTAAAAAT-GTAATTTTTGGAAGT
1 TTTG-GGGTCAAAAATAGG-ATTTTTGGAAGTTTAGGGGTAAAAATAG-AATTTTTGGAAGT
* *
1958612 TTTGAGGTCAAAAATAGGATTTTTGGAAGTTTGGGGGTAAAAATAGAATTTTTGGAAGT
1 TTTGGGGTCAAAAATAGGATTTTTGGAAGTTTAGGGGTAAAAATAGAATTTTTGGAAGT
* * *
1958671 TTTGGTGTCAAAAATAGGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGT
1 TTTGGGGTCAAAAATAGGATTTTTGGAAGTTTAGGGGTAAAAATAGAATTTTTGGAAGT
* * *
1958730 TTCGGGGTAAAAAATAGGATTTTTGGAAGTTCAGGGGT-AAAATAGAATTTTTGGATAGT
1 TTTGGGGTCAAAAATAGGATTTTTGGAAGTTTAGGGGTAAAAATAGAATTTTTGGA-AGT
1958789 TT
1 TT
1958791 AGGGACCTCC
Statistics
Matches: 163, Mismatches: 12, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
58 19 0.12
59 141 0.87
60 3 0.02
ACGTcount: A:0.33, C:0.02, G:0.29, T:0.37
Consensus pattern (59 bp):
TTTGGGGTCAAAAATAGGATTTTTGGAAGTTTAGGGGTAAAAATAGAATTTTTGGAAGT
Found at i:1958634 original size:30 final size:29
Alignment explanation
Indices: 1958553--1958790 Score: 268
Period size: 29 Copynumber: 8.1 Consensus size: 29
1958543 ATTTTAGAGG
*
1958553 TTTGAGGGTAAAAAT-GGAATTTTTGAAAGT
1 TTTG-GGGTAAAAATAGG-ATTTTTGGAAGT
* *
1958583 TTAGGGGTAAAAAT-GTAATTTTTGGAAGT
1 TTTGGGGTAAAAATAG-GATTTTTGGAAGT
*
1958612 TTTGAGGTCAAAAATAGGATTTTTGGAAGT
1 TTTGGGGT-AAAAATAGGATTTTTGGAAGT
* *
1958642 TTGGGGGTAAAAATAGAATTTTTGGAAGT
1 TTTGGGGTAAAAATAGGATTTTTGGAAGT
*
1958671 TTTGGTGTCAAAAATAGGATTTTTGGAAGT
1 TTTGGGGT-AAAAATAGGATTTTTGGAAGT
*
1958701 TTGGGGGTAAAAAT-GGAATTTTTGGAAGT
1 TTTGGGGTAAAAATAGG-ATTTTTGGAAGT
*
1958730 TTCGGGGTAAAAAATAGGATTTTTGGAAGT
1 TTTGGGGT-AAAAATAGGATTTTTGGAAGT
** *
1958760 TCAGGGGT-AAAATAGAATTTTTGGATAGT
1 TTTGGGGTAAAAATAGGATTTTTGGA-AGT
1958789 TT
1 TT
1958791 AGGGACCTCC
Statistics
Matches: 181, Mismatches: 19, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
28 18 0.10
29 83 0.46
30 77 0.43
31 3 0.02
ACGTcount: A:0.33, C:0.02, G:0.29, T:0.37
Consensus pattern (29 bp):
TTTGGGGTAAAAATAGGATTTTTGGAAGT
Found at i:1959816 original size:18 final size:18
Alignment explanation
Indices: 1959782--1959817 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1959772 TTAGTTCCCT
* *
1959782 TTTTTATTATTATTAATA
1 TTTTTATTAATAATAATA
1959800 TTTTTATTAATAATAATA
1 TTTTTATTAATAATAATA
1959818 ATAATAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTTATTAATAATAATA
Found at i:1960546 original size:17 final size:17
Alignment explanation
Indices: 1960521--1960595 Score: 69
Period size: 17 Copynumber: 4.3 Consensus size: 17
1960511 AATTTTATTT
* *
1960521 ATTTAAAATTTATAATA
1 ATTTTAAATTTAAAATA
*
1960538 ATTTTAAATTTGAAAAAA
1 ATTTTAAATTT-AAAATA
* * *
1960556 AATTTAAACTTAAATTA
1 ATTTTAAATTTAAAATA
*
1960573 AATTTAAATTTAAAATAA
1 ATTTTAAATTTAAAAT-A
1960591 ATTTT
1 ATTTT
1960596 TAAACAAATT
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
17 28 0.61
18 18 0.39
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (17 bp):
ATTTTAAATTTAAAATA
Found at i:1962875 original size:25 final size:26
Alignment explanation
Indices: 1962838--1962907 Score: 99
Period size: 25 Copynumber: 2.7 Consensus size: 26
1962828 TAATCAGAGG
1962838 TTTTAAGTCTATTTAAAATT-AA-AA
1 TTTTAAGTCTATTTAAAATTAAAGAA
*
1962862 TTTTAAAGTTTATTTAAAATTAAATGAA
1 TTTT-AAGTCTATTTAAAATTAAA-GAA
1962890 TTTTAAGTCTATTTAAAA
1 TTTTAAGTCTATTTAAAA
1962908 AAATTCATGA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
24 4 0.10
25 15 0.38
26 2 0.05
27 13 0.32
28 6 0.15
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (26 bp):
TTTTAAGTCTATTTAAAATTAAAGAA
Found at i:1963135 original size:42 final size:42
Alignment explanation
Indices: 1963045--1963136 Score: 96
Period size: 42 Copynumber: 2.2 Consensus size: 42
1963035 CAAAAAATTT
* * * *
1963045 AATTAAAATCGATTTTAAATCAAAATAGTAACAAAATAGAAA
1 AATTAAAATCGAATTTAAACCAAAATAATAACAAAATAAAAA
** * *
1963087 TTTTAAAATC-AATTTAAACCGAAATAATAACACAATTAAAAA
1 AATTAAAATCGAATTTAAACCAAAATAATAACA-AAATAAAAA
1963129 AATTAAAA
1 AATTAAAA
1963137 CAAAAATAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
41 18 0.46
42 21 0.54
ACGTcount: A:0.60, C:0.09, G:0.04, T:0.27
Consensus pattern (42 bp):
AATTAAAATCGAATTTAAACCAAAATAATAACAAAATAAAAA
Found at i:1963637 original size:43 final size:43
Alignment explanation
Indices: 1963589--1963695 Score: 155
Period size: 42 Copynumber: 2.5 Consensus size: 43
1963579 TTGTTTTTTG
1963589 TTTTTTTATTTTGTTACTATTTC-GATTTAAAATTGATTTTAAT
1 TTTTTTTATTTTGTTACTATTTCAG-TTTAAAATTGATTTTAAT
1963632 TTTTTTTATTTT-TTACTATTTCAGTTTAAAATTGATTTTAAT
1 TTTTTTTATTTTGTTACTATTTCAGTTTAAAATTGATTTTAAT
*** *
1963674 TAAATTTATTTTGTTATTATTT
1 TTTTTTTATTTTGTTACTATTT
1963696 GGTGTTCTTA
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
42 37 0.64
43 21 0.36
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.64
Consensus pattern (43 bp):
TTTTTTTATTTTGTTACTATTTCAGTTTAAAATTGATTTTAAT
Found at i:1963891 original size:25 final size:25
Alignment explanation
Indices: 1963816--1963892 Score: 84
Period size: 25 Copynumber: 3.0 Consensus size: 25
1963806 GATGACTTTT
*
1963816 TTTTAAGTAGACTTAAAATAAATTTAA
1 TTTTAAATAGACTTAAAAT--ATTTAA
* *
1963843 TTTTAAATAAAATTTAAAA-ATTTAA
1 TTTTAAAT-AGACTTAAAATATTTAA
*
1963868 TTTTAAATAGACTTAAAATCTTTAA
1 TTTTAAATAGACTTAAAATATTTAA
1963893 CTAATAAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
24 8 0.19
25 19 0.45
27 7 0.17
28 8 0.19
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (25 bp):
TTTTAAATAGACTTAAAATATTTAA
Found at i:1965606 original size:29 final size:28
Alignment explanation
Indices: 1965555--1965625 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 28
1965545 AGTCTATATC
* * *
1965555 TTTATAATTTTTAAGGATTAAATCAAAAT
1 TTTATTATTTTTAAGAATAAAAT-AAAAT
* **
1965584 TTTATTATTTTTTAGAATAAAATGTAAT
1 TTTATTATTTTTAAGAATAAAATAAAAT
*
1965612 TTTATTATTATTAA
1 TTTATTATTTTTAA
1965626 TTTAAAATTT
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
28 15 0.44
29 19 0.56
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (28 bp):
TTTATTATTTTTAAGAATAAAATAAAAT
Found at i:1978981 original size:87 final size:87
Alignment explanation
Indices: 1978835--1979008 Score: 348
Period size: 87 Copynumber: 2.0 Consensus size: 87
1978825 TTATATCTGG
1978835 ATATTATATGGCAATTAGAAGAAAAGAATACAATGAATCTGTTCTGTTTTAAACTCATCTGGTTG
1 ATATTATATGGCAATTAGAAGAAAAGAATACAATGAATCTGTTCTGTTTTAAACTCATCTGGTTG
1978900 TAGTTTACTATAATCCTTCCAA
66 TAGTTTACTATAATCCTTCCAA
1978922 ATATTATATGGCAATTAGAAGAAAAGAATACAATGAATCTGTTCTGTTTTAAACTCATCTGGTTG
1 ATATTATATGGCAATTAGAAGAAAAGAATACAATGAATCTGTTCTGTTTTAAACTCATCTGGTTG
1978987 TAGTTTACTATAATCCTTCCAA
66 TAGTTTACTATAATCCTTCCAA
1979009 TAACTTATAG
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.37
Consensus pattern (87 bp):
ATATTATATGGCAATTAGAAGAAAAGAATACAATGAATCTGTTCTGTTTTAAACTCATCTGGTTG
TAGTTTACTATAATCCTTCCAA
Found at i:1985542 original size:3 final size:3
Alignment explanation
Indices: 1985534--1985561 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1985524 ATTCGATATG
1985534 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1985562 TTAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1992421 original size:3 final size:3
Alignment explanation
Indices: 1992413--1992439 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1992403 AGTCGCAATT
1992413 AGG AGG AGG AGG AGG AGG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG
1992440 GGGTGGTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:1994469 original size:20 final size:18
Alignment explanation
Indices: 1994446--1994490 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
1994436 TTTTTTAATT
*
1994446 TTATTTATATTTAAAAATAA
1 TTATTTATA-TAAAAAAT-A
*
1994466 TTATTTTTATAAAAAATA
1 TTATTTATATAAAAAATA
1994484 TTATTTA
1 TTATTTA
1994491 AAAGGAATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 7 0.32
20 8 0.36
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTATTTATATAAAAAATA
Found at i:1994688 original size:3 final size:3
Alignment explanation
Indices: 1994680--1994713 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1994670 TGTAATACCG
1994680 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1994714 GGAACAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1997010 original size:38 final size:38
Alignment explanation
Indices: 1996953--1997054 Score: 132
Period size: 38 Copynumber: 2.7 Consensus size: 38
1996943 ATTTATAAAG
* *
1996953 AGATCTAGCATTTGTTGTAGATTCTCAGGTTACTTAACA
1 AGATCTAGC-CTTGTTGTAGATTCTCAGGTGACTTAACA
* **
1996992 AGATCTAGCCTTGTTGTAGATTCTCGGGTGACTTAATG
1 AGATCTAGCCTTGTTGTAGATTCTCAGGTGACTTAACA
* *
1997030 AGATCAAGCCTTGTTGCAGATTCTC
1 AGATCTAGCCTTGTTGTAGATTCTC
1997055 GAGTTATAAG
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
38 47 0.84
39 9 0.16
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.36
Consensus pattern (38 bp):
AGATCTAGCCTTGTTGTAGATTCTCAGGTGACTTAACA
Found at i:2000439 original size:3 final size:3
Alignment explanation
Indices: 2000431--2000464 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
2000421 CCTTGTTGCA
*
2000431 CTT CTT CTT CTT CCT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
2000465 AGTCTTCACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:2006030 original size:17 final size:17
Alignment explanation
Indices: 2005988--2006030 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2005978 CTTATTAATT
2005988 TTTTTAGTTGACTTATTA
1 TTTTTA-TTGACTTATTA
* * *
2006006 TATGTATTTACTTATTA
1 TTTTTATTGACTTATTA
2006023 TTTTTATT
1 TTTTTATT
2006031 ATATATGATT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.65
Consensus pattern (17 bp):
TTTTTATTGACTTATTA
Found at i:2009317 original size:39 final size:39
Alignment explanation
Indices: 2009274--2009354 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 39
2009264 TAAAATCTTC
* *
2009274 ATAATAATTTA-ATATTTTAATAAATATTTAATAATTT-TT
1 ATAAT-ATTTATAAATTTTAAT-AAGATTTAATAATTTGTT
*
2009313 ATAATGTTTATAAATTTTAATAAGATTTAATAATTTGTT
1 ATAATATTTATAAATTTTAATAAGATTTAATAATTTGTT
2009352 ATA
1 ATA
2009355 TTTATTGTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 18 0.49
39 19 0.51
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (39 bp):
ATAATATTTATAAATTTTAATAAGATTTAATAATTTGTT
Found at i:2009345 original size:29 final size:29
Alignment explanation
Indices: 2009275--2009348 Score: 84
Period size: 28 Copynumber: 2.6 Consensus size: 29
2009265 AAAATCTTCA
2009275 TAAT-AATTTAAT-ATTTTAATAAATATT
1 TAATAAATTTAATAATTTTAATAAATATT
* *
2009302 TAATAATTTTTATAATGTTT-ATAAAT-TT
1 TAATAAATTTAATAAT-TTTAATAAATATT
2009330 TAATAAGATTTAATAATTT
1 TAATAA-ATTTAATAATTT
2009349 GTTATATTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
27 4 0.10
28 16 0.41
29 16 0.41
30 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (29 bp):
TAATAAATTTAATAATTTTAATAAATATT
Found at i:2009347 original size:19 final size:19
Alignment explanation
Indices: 2009280--2009348 Score: 72
Period size: 19 Copynumber: 3.6 Consensus size: 19
2009270 CTTCATAATA
*
2009280 ATTTAAT-ATTTTAATAAAT
1 ATTTAATAATTTTAAT-AAG
*
2009299 ATTTAATAATTTTTATAATG
1 ATTTAATAATTTTAATAA-G
2009319 -TTT-ATAAATTTTAATAAG
1 ATTTAAT-AATTTTAATAAG
2009337 ATTTAATAATTT
1 ATTTAATAATTT
2009349 GTTATATTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
18 3 0.07
19 30 0.71
20 9 0.21
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
ATTTAATAATTTTAATAAG
Found at i:2009587 original size:8 final size:8
Alignment explanation
Indices: 2009574--2009600 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
2009564 GAAATTAAAA
2009574 TTAATTAT
1 TTAATTAT
2009582 TTAATTAT
1 TTAATTAT
2009590 TTAATTAT
1 TTAATTAT
2009598 TTA
1 TTA
2009601 GAGTTTTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TTAATTAT
Found at i:2011582 original size:24 final size:22
Alignment explanation
Indices: 2011554--2011598 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
2011544 TATTATTTTT
2011554 AAATGA-AAATATCGAAAATAATTA
1 AAATGAGAAA-ATC-AAAA-AATTA
2011578 AAATGAGAAAATCAAAAAATT
1 AAATGAGAAAATCAAAAAATT
2011599 GTTAGTGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.20
23 4 0.20
24 9 0.45
25 3 0.15
ACGTcount: A:0.64, C:0.04, G:0.09, T:0.22
Consensus pattern (22 bp):
AAATGAGAAAATCAAAAAATTA
Found at i:2012030 original size:18 final size:17
Alignment explanation
Indices: 2012004--2012060 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
2011994 TTTAGACCAC
*
2012004 AATTAAAAATTATAAAA
1 AATTTAAAATTATAAAA
2012021 TAATTTAAAAATATATAAAA
1 -AATTT-AAAAT-TATAAAA
* *
2012041 AAGTTAAAATTAAAAAA
1 AATTTAAAATTATAAAA
2012058 AAT
1 AAT
2012061 CAAAATAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
17 8 0.24
18 9 0.27
19 9 0.27
20 7 0.21
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (17 bp):
AATTTAAAATTATAAAA
Found at i:2012037 original size:20 final size:18
Alignment explanation
Indices: 2012006--2012058 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
2011996 TAGACCACAA
*
2012006 TTAAAAATTATAAAATAAT
1 TTAAAAATTATAAAA-AAG
2012025 TTAAAAATATATAAAAAAG
1 TTAAAAAT-TATAAAAAAG
2012044 TT-AAAATTA-AAAAAA
1 TTAAAAATTATAAAAAA
2012059 ATCAAAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
16 6 0.19
17 2 0.06
18 5 0.16
19 12 0.38
20 7 0.22
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
TTAAAAATTATAAAAAAG
Found at i:2020323 original size:26 final size:27
Alignment explanation
Indices: 2020279--2020329 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
2020269 TAAATTTAAA
2020279 AAAAAAAAATTAATCGAACC-AAATTT
1 AAAAAAAAATTAATCGAACCGAAATTT
*
2020305 AAAAAAAATTTAA-CTGAACCGAAAT
1 AAAAAAAAATTAATC-GAACCGAAAT
2020330 ATTTGGTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 1 0.05
26 17 0.77
27 4 0.18
ACGTcount: A:0.61, C:0.12, G:0.06, T:0.22
Consensus pattern (27 bp):
AAAAAAAAATTAATCGAACCGAAATTT
Found at i:2026437 original size:6 final size:6
Alignment explanation
Indices: 2026426--2026454 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2026416 GATGGGAAGG
2026426 GGGTGT GGGTGT GGGTGT GGGTGT GGGTG
1 GGGTGT GGGTGT GGGTGT GGGTGT GGGTG
2026455 GCGGCTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.69, T:0.31
Consensus pattern (6 bp):
GGGTGT
Found at i:2026596 original size:3 final size:3
Alignment explanation
Indices: 2026588--2026613 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2026578 CGAACTTCAA
2026588 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
2026614 AACATAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:2033300 original size:17 final size:18
Alignment explanation
Indices: 2033259--2033303 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
2033249 TTTTTTCTTT
*
2033259 TTTTCTTTTTCATCTATTC
1 TTTTC-TTTTCATCAATTC
*
2033278 TTTTCTTTTCAT-AATTG
1 TTTTCTTTTCATCAATTC
2033295 TTTTCTTTT
1 TTTTCTTTT
2033304 ATTCCTTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 12 0.50
18 7 0.29
19 5 0.21
ACGTcount: A:0.11, C:0.16, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTTCTTTTCATCAATTC
Found at i:2036263 original size:21 final size:21
Alignment explanation
Indices: 2036237--2036279 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2036227 ACCTTTAAAC
2036237 GACCTTCAAAATCGGGTTTGT
1 GACCTTCAAAATCGGGTTTGT
**
2036258 GACCTTCAGGATCGGGTTTGT
1 GACCTTCAAAATCGGGTTTGT
2036279 G
1 G
2036280 CACAATATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.33
Consensus pattern (21 bp):
GACCTTCAAAATCGGGTTTGT
Found at i:2040669 original size:15 final size:15
Alignment explanation
Indices: 2040651--2040680 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2040641 TATTAAGTTA
2040651 TTTTATTTTTCAAAT
1 TTTTATTTTTCAAAT
*
2040666 TTTTATTTTTGAAAT
1 TTTTATTTTTCAAAT
2040681 AAGTTATTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTTATTTTTCAAAT
Done.