Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014177.1 Kokia drynarioides strain JFW-HI SEQ_129210, 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: 757717
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 61 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:522674 original size:17 final size:17
Alignment explanation
Indices: 522652--522684 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
522642 GAATATTTTT
522652 TATTTTTATTTTTTTCG
1 TATTTTTATTTTTTTCG
*
522669 TATTTTTCTTTTTTTC
1 TATTTTTATTTTTTTC
522685 TCGACTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.79
Consensus pattern (17 bp):
TATTTTTATTTTTTTCG
Found at i:534293 original size:33 final size:33
Alignment explanation
Indices: 534256--534324 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
534246 GTTCTAATTC
* *
534256 TAAAAATTTAATCATCAACATTTACAGATCCTA
1 TAAAAATTTAATAATCAACATTTACACATCCTA
534289 TAAAAATTTAATAATCAACATTTACACATCCTA
1 TAAAAATTTAATAATCAACATTTACACATCCTA
534322 TAA
1 TAA
534325 TTTGATCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.01, T:0.33
Consensus pattern (33 bp):
TAAAAATTTAATAATCAACATTTACACATCCTA
Found at i:542026 original size:2 final size:2
Alignment explanation
Indices: 542019--542063 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
542009 AGAATTCAGA
* *
542019 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC GC TC TT TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
542061 TC T
1 TC T
542064 ATTTTCAACT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.47, G:0.02, T:0.51
Consensus pattern (2 bp):
TC
Found at i:542436 original size:29 final size:27
Alignment explanation
Indices: 542404--542470 Score: 71
Period size: 31 Copynumber: 2.3 Consensus size: 27
542394 TAAATCTCAA
* *
542404 AATTATACATTAATTTTGATGTAATGTGT
1 AATTATACATAAATTTTAAT-TAA-GTGT
*
542433 AATTGTATACATAAATTTTAATTTAGTGT
1 AA-T-TATACATAAATTTTAATTAAGTGT
542462 AATTATACA
1 AATTATACA
542471 CGTGAAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 6 0.18
28 1 0.03
29 8 0.24
30 3 0.09
31 15 0.45
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.46
Consensus pattern (27 bp):
AATTATACATAAATTTTAATTAAGTGT
Found at i:543161 original size:19 final size:18
Alignment explanation
Indices: 543137--543179 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
543127 TAACGTTATT
*
543137 TTTATTTTGATTACTTTAA
1 TTTATTTTGATTAATTT-A
*
543156 TTTATTTTTATTAATTTA
1 TTTATTTTGATTAATTTA
543174 TTTATT
1 TTTATT
543180 ATAGTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTATTTTGATTAATTTA
Found at i:543169 original size:14 final size:15
Alignment explanation
Indices: 543152--543181 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
543142 TTTGATTACT
543152 TTAATTTATTT-TTA
1 TTAATTTATTTATTA
543166 TTAATTTATTTATTA
1 TTAATTTATTTATTA
543181 T
1 T
543182 AGTTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTAATTTATTTATTA
Found at i:547187 original size:15 final size:15
Alignment explanation
Indices: 547128--547192 Score: 50
Period size: 15 Copynumber: 4.5 Consensus size: 15
547118 AAGAAATAAA
547128 ATAA-AATAACAATG
1 ATAATAATAACAATG
*
547142 CA-AAAAATAA-AATG
1 -ATAATAATAACAATG
*
547156 ATAGT--TAACAGATG
1 ATAATAATAACA-ATG
547170 ATAATAATAACAATG
1 ATAATAATAACAATG
*
547185 ATAGTAAT
1 ATAATAAT
547193 GGCAAAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
12 3 0.08
13 2 0.05
14 14 0.35
15 16 0.40
16 5 0.12
ACGTcount: A:0.58, C:0.06, G:0.11, T:0.25
Consensus pattern (15 bp):
ATAATAATAACAATG
Found at i:547428 original size:4 final size:4
Alignment explanation
Indices: 547419--547469 Score: 54
Period size: 4 Copynumber: 12.8 Consensus size: 4
547409 GTAAATGACA
547419 AAAT AAAT AAAT AAAT AAA- ATAAT AAAAT AAA- AAAT AAAT ACAA- AAAT
1 AAAT AAAT AAAT AAAT AAAT A-AAT -AAAT AAAT AAAT AAAT A-AAT AAAT
547467 AAA
1 AAA
547470 AAAAGGGTAG
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
3 6 0.15
4 29 0.71
5 5 0.12
6 1 0.02
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:547434 original size:12 final size:11
Alignment explanation
Indices: 547419--547473 Score: 67
Period size: 12 Copynumber: 4.7 Consensus size: 11
547409 GTAAATGACA
547419 AAATAAATAAAT
1 AAATAAA-AAAT
547431 AAATAAAATAAT
1 AAATAAAA-AAT
547443 AAAATAAAAAAT
1 -AAATAAAAAAT
547455 AAATACAAAAAT
1 AAATA-AAAAAT
547467 AAA-AAAA
1 AAATAAAA
547474 GGGTAGACAA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 3 0.08
11 7 0.17
12 22 0.55
13 8 0.20
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (11 bp):
AAATAAAAAAT
Found at i:547997 original size:21 final size:21
Alignment explanation
Indices: 547973--548013 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
547963 CTTTTTTTGC
*
547973 AAAAAAT-TCATTTTTTTTCTA
1 AAAAAATATC-TTTATTTTCTA
547994 AAAAAATATCTTTATTTTCT
1 AAAAAATATCTTTATTTTCT
548014 TTTTTTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (21 bp):
AAAAAATATCTTTATTTTCTA
Found at i:549464 original size:50 final size:50
Alignment explanation
Indices: 549378--549849 Score: 204
Period size: 51 Copynumber: 9.3 Consensus size: 50
549368 AACGAGATAA
* *
549378 GATTTGCTTTTGTAGCTTCAATCCGACCCA-TAGCAACTTTAGAGGTATAG
1 GATTTGCTTTTGTAGCTTCAATCTGACCCACT-GCAACTTCAGAGGTATAG
* * * *
549428 GATTTGGTTTTGTAGCTTC-ATCTTACTCCACTGCAACTTCA-AGGAAATAAA
1 GATTTGCTTTTGTAGCTTCAATCTGAC-CCACTGCAACTTCAGAGG-TAT-AG
* * *
549479 GATTTGCTTCTGTAGCTTCAATCTGACCCACTGTAACTTCAGGGGTATAG
1 GATTTGCTTTTGTAGCTTCAATCTGACCCACTGCAACTTCAGAGGTATAG
* *
549529 GATTTGACATTTTGTAG-TCTC-ATCTTG-CTCTACTGCAACTTCAGAGAG-ATAAA
1 GATTTG-C-TTTTGTAGCT-TCAATC-TGAC-CCACTGCAACTTCAGAG-GTAT-AG
** * ** * * * * * *
549582 GATTTGCCATCGTAATTTTTAGTCTAATCTATTGCAACTTCA-AGGATATAG
1 GATTTGCTTTTGT-AGCTTCAATCTGACCCACTGCAACTTCAGAGG-TATAG
* * ** * * * * *
549633 GATTTGATGTCATAACTTC-ATCTTG-CTCCACTACAACTTTAG-GGAGATAAA
1 GATTTGCTTTTGTAGCTTCAATC-TGAC-CCACTGCAACTTCAGAGG-TAT-AG
* * * * *
549684 GATTTGCTTTTGTAGC-TCTATCCG-CCCACTACAACTTTA-AGGATATAA
1 GATTTGCTTTTGTAGCTTCAATCTGACCCACTGCAACTTCAGAGG-TATAG
* * * * * * *
549732 GATTTGATATTGTAG-TCTC-ATCTTACTCCACTGTAACTACA-AGGAAATAAA
1 GATTTGCTTTTGTAGCT-TCAATCTGAC-CCACTGCAACTTCAGAGG-TAT-AG
* *
549783 GATTTGCTTCTGTAGCTTCAATCTGACCCACTGCAACTTCAGGGGTATAG
1 GATTTGCTTTTGTAGCTTCAATCTGACCCACTGCAACTTCAGAGGTATAG
549833 GATTTGACATTTTGTAG
1 GATTTG-C-TTTTGTAG
549850 TCTTTTATTG
Statistics
Matches: 317, Mismatches: 70, Indels: 68
0.70 0.15 0.15
Matches are distributed among these distances:
48 18 0.06
49 32 0.10
50 85 0.27
51 101 0.32
52 70 0.22
53 11 0.03
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (50 bp):
GATTTGCTTTTGTAGCTTCAATCTGACCCACTGCAACTTCAGAGGTATAG
Found at i:549497 original size:51 final size:50
Alignment explanation
Indices: 549304--549838 Score: 249
Period size: 50 Copynumber: 10.6 Consensus size: 50
549294 TTTAATTTTA
* * * * * ** *
549304 TCCACTACAACTTCAGGGATATAGGATTTAACATC-GTAAATTCATCTTGC
1 TCCACTGCAACTTCAAGGATATAAGATTT-GCTTCTGTAGCTTCATCTTAC
* * * * **
549354 CCCACTGCATA-TTCAACGAGATAAGATTTGCTTTTGTAGCTTCAATCCGAC
1 TCCACTGCA-ACTTCAAGGATATAAGATTTGCTTCTGTAGCTTC-ATCTTAC
* * * *
549405 -CCA-TAGCAACTTTAGAGG-TATAGGATTTGGTTTTGTAGCTTCATCTTAC
1 TCCACT-GCAACTTCA-AGGATATAAGATTTGCTTCTGTAGCTTCATCTTAC
* *
549454 TCCACTGCAACTTCAAGGAAATAAAGATTTGCTTCTGTAGCTTCAATCTGAC
1 TCCACTGCAACTTCAAGGATAT-AAGATTTGCTTCTGTAGCTTC-ATCTTAC
* * * * * *
549506 -CCACTGTAACTTCAGGGGTATAGGATTTGACATTTTGTAG-TCTCATCTTGC
1 TCCACTGCAACTTCAAGGATATAAGATTTG-C-TTCTGTAGCT-TCATCTTAC
* * ** * *
549557 TCTACTGCAACTTCAGAGAGATA-AAGATTTGCCATC-GTAATTTTTAGTC-TAA
1 TCCACTGCAACTTCA-AG-GATATAAGATTTG-CTTCTGT-AGCTTCA-TCTTAC
* * * * * * *
549609 TCTATTGCAACTTCAAGGATATAGGATTTGATGTC-ATAACTTCATCTTGC
1 TCCACTGCAACTTCAAGGATATAAGATTTGCT-TCTGTAGCTTCATCTTAC
* * * * * **
549659 TCCACTACAACTTTAGGGAGATAAAGATTTGCTTTTGTAGC-TCTATC-CGC
1 TCCACTGCAACTTCAAGGATAT-AAGATTTGCTTCTGTAGCTTC-ATCTTAC
* * *
549709 -CCACTACAACTTTAAGGATATAAGATTTGATAT-TGTAG-TCTCATCTTAC
1 TCCACTGCAACTTCAAGGATATAAGATTTGCT-TCTGTAGCT-TCATCTTAC
* * * *
549758 TCCACTGTAACTACAAGGAAATAAAGATTTGCTTCTGTAGCTTCAATCTGAC
1 TCCACTGCAACTTCAAGGATAT-AAGATTTGCTTCTGTAGCTTC-ATCTTAC
* * *
549810 -CCACTGCAACTTCAGGGGTATAGGATTTG
1 TCCACTGCAACTTCAAGGATATAAGATTTG
549839 ACATTTTGTA
Statistics
Matches: 363, Mismatches: 87, Indels: 70
0.70 0.17 0.13
Matches are distributed among these distances:
48 17 0.05
49 37 0.10
50 131 0.36
51 110 0.30
52 53 0.15
53 12 0.03
54 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (50 bp):
TCCACTGCAACTTCAAGGATATAAGATTTGCTTCTGTAGCTTCATCTTAC
Found at i:549761 original size:99 final size:100
Alignment explanation
Indices: 549305--550094 Score: 515
Period size: 99 Copynumber: 7.8 Consensus size: 100
549295 TTAATTTTAT
* * * * * * *
549305 CCACTACAACTTCAGGGATATAGGATTTAACATCGTAAAT-TCATCTTGCCCCACTGCATA-TTC
1 CCACTACAACTTCAGGGATATAAGATTTGATATTGT-AGTCTCATCTTGCTCCACTACA-ACTTC
** * * *
549368 AACGAGAT-AAGATTTGCTTTTGTAGCTTCAATCCGAC
64 AGGGAGATAAAGATTTGCTTCTGTAGC-TCTATCCAAC
* * * * * *
549405 CCA-TAGCAACTTTAGAGG-TATAGGATTTGGTTTTGTAG-CTTCATCTTACTCCACTGCAACTT
1 CCACTA-CAACTTCAG-GGATATAAGATTTGATATTGTAGTC-TCATCTTGCTCCACTACAACTT
* * * **
549467 CAAGGAAATAAAGATTTGCTTCTGTAGCTTCAATCTGAC
63 CAGGGAGATAAAGATTTGCTTCTGTAGC-TCTATCCAAC
** * * * * *
549506 CCACTGTAACTTCAGGGGTATAGGATTTGACATTTTGTAGTCTCATCTTGCTCTACTGCAACTTC
1 CCACTACAACTTCAGGGATATAAGATTTG--ATATTGTAGTCTCATCTTGCTCCACTACAACTTC
* * ** * * *
549571 AGAGAGATAAAGATTTGCCATC-GTAATTTTTAGTCTAAT
64 AGGGAGATAAAGATTTG-CTTCTGT-AGCTCTA-TCCAAC
* * * * * * ** * *
549610 CTATTGCAACTTCAAGGATATAGGATTTGATGTCATA-ACTTCATCTTGCTCCACTACAACTTTA
1 CCACTACAACTTCAGGGATATAAGATTTGATATTGTAGTC-TCATCTTGCTCCACTACAACTTCA
* *
549674 GGGAGATAAAGATTTGCTTTTGTAGCTCTATCC-GC
65 GGGAGATAAAGATTTGCTTCTGTAGCTCTATCCAAC
* * * ** * *
549709 CCACTACAACTTTAAGGATATAAGATTTGATATTGTAGTCTCATCTTACTCCACTGTAACTACAA
1 CCACTACAACTTCAGGGATATAAGATTTGATATTGTAGTCTCATCTTGCTCCACTACAACTTCAG
* * **
549774 GGAAATAAAGATTTGCTTCTGTAGCTTCAATCTGAC
66 GGAGATAAAGATTTGCTTCTGTAGC-TCTATCCAAC
* * * * ** * *
549810 CCACTGCAACTTCAGGGGTATAGGATTTGACATTTTGTAGTCTTTTATTGCTCTACTACAACTTC
1 CCACTACAACTTCAGGGATATAAGATTTG--ATATTGTAGTCTCATCTTGCTCCACTACAACTTC
* ** ** * *
549875 AGAGAGATAAAGATTTGCCACTGTAATTTTTAGTCCAAT
64 AGGGAGATAAAGATTTGCTTCTGT-AGCTCTA-TCCAAC
* * ** **
549914 CCACT-CTAACTTCAGGGATATAGGATTTGATGTCATAACCTCATCTTGCTCCACTACAACTT-A
1 CCACTAC-AACTTCAGGGATATAAGATTTGATATTGTAGTCTCATCTTGCTCCACTACAACTTCA
* *
549977 GGGAGATAGAGATTTGCTTTTGTAGCTCTATCCAAC
65 GGGAGATAAAGATTTGCTTCTGTAGCTCTATCCAAC
* * * **
550013 CCATTACAACTTCAGGGGTATAAGATTTCG-TATTGTAGTCTCATCTTGCTCTACTGTAACTTCA
1 CCACTACAACTTCAGGGATATAAGATTT-GATATTGTAGTCTCATCTTGCTCCACTACAACTTCA
*
550077 GAGAGATAAAGATTTGCT
65 GGGAGATAAAGATTTGCT
550095 ATCGTAATTT
Statistics
Matches: 535, Mismatches: 128, Indels: 54
0.75 0.18 0.08
Matches are distributed among these distances:
99 127 0.24
100 82 0.15
101 101 0.19
102 68 0.13
103 94 0.18
104 63 0.12
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (100 bp):
CCACTACAACTTCAGGGATATAAGATTTGATATTGTAGTCTCATCTTGCTCCACTACAACTTCAG
GGAGATAAAGATTTGCTTCTGTAGCTCTATCCAAC
Found at i:549777 original size:304 final size:300
Alignment explanation
Indices: 549303--550094 Score: 1083
Period size: 304 Copynumber: 2.6 Consensus size: 300
549293 TTTTAATTTT
* ** * * * *
549303 ATCCACTACAACTTCAGGGATATAGGATTTAACATCGTAAATTCATCTTGCCCCACTGCATA-TT
1 ATCCACT-CAACTTCAGGGATATAGGATTTGATGTCATAACTTCATCTTGCTCCACTACA-ACTT
* ** * *
549367 CAACGAGAT-AAGATTTGCTTTTGTAGCTTCAATCCGACCCATAGCAACTTTAGAGGTATAGGAT
64 TAGGGAGATAAAGATTTGCTTTTGTAGC-TCTATCCG-CCCATA-CAACTTTA-AGGTATAAGAT
* *
549431 TTGGTTTTGTAG-CTTCATCTTACTCCACTGCAACTTCAAGGAAATAAAGATTTGCTTCTGTAGC
125 TT-GTATTGTAGTC-TCATCTTACTCCACTGTAACTTCAAGGAAATAAAGATTTGCTTCTGTAGC
* *
549495 TTCAATCTGACCCACTGTAACTTCAGGGGTATAGGATTTGACATTTTGTAGTCTCATCTTGCTCT
188 TTCAATCTGACCCACTGCAACTTCAGGGGTATAGGATTTGACATTTTGTAGTCTCATATTGCTCT
* *
549560 ACTGCAACTTCAGAGAGATAAAGATTTGCCA-TCGTAATTTTTAGTCTA
253 ACTACAACTTCAGAGAGATAAAGATTTGCCACT-GTAATTTTTAGTCCA
* * *
549608 ATCTATTGCAACTTCAAGGATATAGGATTTGATGTCATAACTTCATCTTGCTCCACTACAACTTT
1 ATCCACT-CAACTTCAGGGATATAGGATTTGATGTCATAACTTCATCTTGCTCCACTACAACTTT
549673 AGGGAGATAAAGATTTGCTTTTGTAGCTCTATCCGCCCACTACAACTTTAAGGATATAAGATTTG
65 AGGGAGATAAAGATTTGCTTTTGTAGCTCTATCCGCCCA-TACAACTTTAAGG-TATAAGATTTG
*
549738 ATATTGTAGTCTCATCTTACTCCACTGTAACTACAAGGAAATAAAGATTTGCTTCTGTAGCTTCA
128 -TATTGTAGTCTCATCTTACTCCACTGTAACTTCAAGGAAATAAAGATTTGCTTCTGTAGCTTCA
**
549803 ATCTGACCCACTGCAACTTCAGGGGTATAGGATTTGACATTTTGTAGTCTTTTATTGCTCTACTA
192 ATCTGACCCACTGCAACTTCAGGGGTATAGGATTTGACATTTTGTAGTCTCATATTGCTCTACTA
549868 CAACTTCAGAGAGATAAAGATTTGCCACTGTAATTTTTAGTCCA
257 CAACTTCAGAGAGATAAAGATTTGCCACTGTAATTTTTAGTCCA
*
549912 ATCCACTCTAACTTCAGGGATATAGGATTTGATGTCATAACCTCATCTTGCTCCACTACAAC-TT
1 ATCCACTC-AACTTCAGGGATATAGGATTTGATGTCATAACTTCATCTTGCTCCACTACAACTTT
* * * *
549976 AGGGAGATAGAGATTTGCTTTTGTAGCTCTATCCAACCCATTACAACTTCAGGGGTATAAGATTT
65 AGGGAGATAAAGATTTGCTTTTGTAGCTCTATCC-GCCCA-TACAACTTTA-AGGTATAAGATTT
* * *
550041 CGTATTGTAGTCTCATCTTGCTCTACTGTAACTTC-AGAGAGATAAAGATTTGCT
127 -GTATTGTAGTCTCATCTTACTCCACTGTAACTTCAAG-GAAATAAAGATTTGCT
550095 ATCGTAATTT
Statistics
Matches: 437, Mismatches: 38, Indels: 25
0.87 0.08 0.05
Matches are distributed among these distances:
303 42 0.10
304 306 0.70
305 71 0.16
306 18 0.04
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (300 bp):
ATCCACTCAACTTCAGGGATATAGGATTTGATGTCATAACTTCATCTTGCTCCACTACAACTTTA
GGGAGATAAAGATTTGCTTTTGTAGCTCTATCCGCCCATACAACTTTAAGGTATAAGATTTGTAT
TGTAGTCTCATCTTACTCCACTGTAACTTCAAGGAAATAAAGATTTGCTTCTGTAGCTTCAATCT
GACCCACTGCAACTTCAGGGGTATAGGATTTGACATTTTGTAGTCTCATATTGCTCTACTACAAC
TTCAGAGAGATAAAGATTTGCCACTGTAATTTTTAGTCCA
Found at i:550976 original size:19 final size:19
Alignment explanation
Indices: 550954--551007 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 19
550944 CATCTTGACC
550954 TCTCCTTTTCTTTTTCTTT
1 TCTCCTTTTCTTTTTCTTT
*
550973 TCTCTTTTTCTTTTTCTTT
1 TCTCCTTTTCTTTTTCTTT
550992 T-T-CTTTT-TTTTT-TTT
1 TCTCCTTTTCTTTTTCTTT
551007 T
1 T
551008 GGGTGAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 4 0.12
16 5 0.15
17 4 0.12
18 1 0.03
19 19 0.58
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (19 bp):
TCTCCTTTTCTTTTTCTTT
Found at i:551007 original size:6 final size:6
Alignment explanation
Indices: 550959--551004 Score: 76
Period size: 6 Copynumber: 7.7 Consensus size: 6
550949 TGACCTCTCC
550959 TTTTCT TTTTCT TTTCTCT TTTTCT TTTTCT TTTTCT TTTT-T TTTT
1 TTTTCT TTTTCT TTT-TCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
551005 TTTGGGTGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.13
6 28 0.72
7 6 0.15
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTCT
Found at i:557815 original size:10 final size:10
Alignment explanation
Indices: 557802--557860 Score: 52
Period size: 10 Copynumber: 6.0 Consensus size: 10
557792 TATATATATA
557802 TTCTTTCTTT
1 TTCTTTCTTT
557812 TTCTTTCTTT
1 TTCTTTCTTT
* **
557822 TTATCAAC-TT
1 TTCT-TTCTTT
557832 TTCTTTC-TT
1 TTCTTTCTTT
557841 TT-TTTCTTT
1 TTCTTTCTTT
557850 TTCTTTTCTTT
1 TTC-TTTCTTT
557861 ATGCAACTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
8 4 0.10
9 9 0.23
10 18 0.46
11 8 0.21
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (10 bp):
TTCTTTCTTT
Found at i:575113 original size:34 final size:34
Alignment explanation
Indices: 575070--575135 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
575060 TTCACATGGT
575070 GCGGTGACAATTAAAGATTTGAATGATGGCCATC
1 GCGGTGACAATTAAAGATTTGAATGATGGCCATC
575104 GCGGTGACAATTAAAGATTTGAATGATGGCCA
1 GCGGTGACAATTAAAGATTTGAATGATGGCCA
575136 CCAATTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.33, C:0.14, G:0.27, T:0.26
Consensus pattern (34 bp):
GCGGTGACAATTAAAGATTTGAATGATGGCCATC
Found at i:577397 original size:12 final size:13
Alignment explanation
Indices: 577377--577424 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
577367 AGAAGAAAAG
577377 CAAAGAGAAGCAC
1 CAAAGAGAAGCAC
* *
577390 CAAA-AGAAGAAAG
1 CAAAGAGAAG-CAC
577403 CAAAGAGAAGCAC
1 CAAAGAGAAGCAC
577416 CAAA-AGAAG
1 CAAAGAGAAG
577425 AAAAAGAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
12 10 0.34
13 14 0.48
14 5 0.17
ACGTcount: A:0.60, C:0.17, G:0.23, T:0.00
Consensus pattern (13 bp):
CAAAGAGAAGCAC
Found at i:577409 original size:26 final size:26
Alignment explanation
Indices: 577364--577427 Score: 119
Period size: 26 Copynumber: 2.4 Consensus size: 26
577354 AAAAGAAAAG
577364 AAAAGAAGAAAAGCAAAGAGAAGCACC
1 AAAAGAAG-AAAGCAAAGAGAAGCACC
577391 AAAAGAAGAAAGCAAAGAGAAGCACC
1 AAAAGAAGAAAGCAAAGAGAAGCACC
577417 AAAAGAAGAAA
1 AAAAGAAGAAA
577428 AAGAAATCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 29 0.78
27 8 0.22
ACGTcount: A:0.66, C:0.12, G:0.22, T:0.00
Consensus pattern (26 bp):
AAAAGAAGAAAGCAAAGAGAAGCACC
Found at i:577421 original size:14 final size:14
Alignment explanation
Indices: 577378--577422 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
577368 GAAGAAAAGC
577378 AAAGAGAAGCACCA
1 AAAGAGAAGCACCA
*
577392 AAAGAAGAA--AGC-
1 AAAG-AGAAGCACCA
577404 AAAGAGAAGCACCA
1 AAAGAGAAGCACCA
577418 AAAGA
1 AAAGA
577423 AGAAAAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
11 4 0.16
12 4 0.16
13 4 0.16
14 9 0.36
15 4 0.16
ACGTcount: A:0.62, C:0.16, G:0.22, T:0.00
Consensus pattern (14 bp):
AAAGAGAAGCACCA
Found at i:598774 original size:18 final size:18
Alignment explanation
Indices: 598748--598782 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
598738 TGGCTACATA
*
598748 TGAGCATGTGACTGCATC
1 TGAGCATGTGACAGCATC
*
598766 TGAGTATGTGACAGCAT
1 TGAGCATGTGACAGCAT
598783 ATGATCATGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (18 bp):
TGAGCATGTGACAGCATC
Found at i:607653 original size:24 final size:24
Alignment explanation
Indices: 607620--607674 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
607610 GTTAAGAGTA
*
607620 AAAATTGTCAGTGCAAATGAAATAC
1 AAAA-TGTCAGTACAAATGAAATAC
* * *
607645 AAAATGTCAGTACAACTGTAATAT
1 AAAATGTCAGTACAAATGAAATAC
607669 AAAATG
1 AAAATG
607675 AATTGATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.25
Consensus pattern (24 bp):
AAAATGTCAGTACAAATGAAATAC
Found at i:610140 original size:3 final size:3
Alignment explanation
Indices: 610134--610190 Score: 64
Period size: 3 Copynumber: 19.0 Consensus size: 3
610124 GGCAACATCA
* *
610134 TCT TCT TCT TTT TCT TCCT TCT T-T TCT TTT TCT TCT TCT T-T TCTT
1 TCT TCT TCT TCT TCT T-CT TCT TCT TCT TCT TCT TCT TCT TCT TC-T
610179 TCT TCT TCT TCT
1 TCT TCT TCT TCT
610191 ATCTCAATAC
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 4 0.09
3 36 0.78
4 6 0.13
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
TCT
Found at i:610162 original size:18 final size:17
Alignment explanation
Indices: 610134--610190 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 17
610124 GGCAACATCA
610134 TCTTCTTCTTTTTCTTCCT
1 TCTT-TTCTTTTTCTT-CT
610153 TCTTTTCTTTTTCTTCT
1 TCTTTTCTTTTTCTTCT
610170 TCTTTTCTTTCTTCTTCT
1 TCTTTTCTTT-TTCTTCT
610188 TCT
1 TCT
610191 ATCTCAATAC
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
17 12 0.32
18 21 0.57
19 4 0.11
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (17 bp):
TCTTTTCTTTTTCTTCT
Found at i:616242 original size:18 final size:18
Alignment explanation
Indices: 616191--616251 Score: 86
Period size: 18 Copynumber: 3.4 Consensus size: 18
616181 TTGTTATGGT
*
616191 TGCATCTGAGTATGCGAC
1 TGCATCTGAGTATGTGAC
616209 TGCATCTGAGTATGTGAC
1 TGCATCTGAGTATGTGAC
* * *
616227 TGCATCTGATTTTGTGAT
1 TGCATCTGAGTATGTGAC
616245 TGCATCT
1 TGCATCT
616252 AATCAGGCTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (18 bp):
TGCATCTGAGTATGTGAC
Found at i:617786 original size:24 final size:24
Alignment explanation
Indices: 617758--617805 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
617748 GTAAAAATTA
617758 TCAGTGCAAATGTAATACAAAATG
1 TCAGTGCAAATGTAATACAAAATG
* *
617782 TCAGTGCAACTGTAATATAAAATG
1 TCAGTGCAAATGTAATACAAAATG
617806 AATTGATTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (24 bp):
TCAGTGCAAATGTAATACAAAATG
Found at i:628529 original size:36 final size:36
Alignment explanation
Indices: 628476--628579 Score: 154
Period size: 36 Copynumber: 2.9 Consensus size: 36
628466 TAGTAACAAA
* *
628476 CATGACCTTTGGTTCAATAGGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAATAGGGAGTAAAACGAGCAT
* * *
628512 CATGACCTCTGGGTCAATAGGAAGTTAAACGAGCAT
1 CATGACCTTTGGGTCAATAGGGAGTAAAACGAGCAT
*
628548 TATGACCTTTGGGTCAATAGGGAGTAAAACGA
1 CATGACCTTTGGGTCAATAGGGAGTAAAACGA
628580 ATAACGAACG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (36 bp):
CATGACCTTTGGGTCAATAGGGAGTAAAACGAGCAT
Found at i:630064 original size:15 final size:16
Alignment explanation
Indices: 630030--630071 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
630020 TTCATTTCAT
*
630030 TTTATATATTTATCTA
1 TTTATTTATTTATCTA
*
630046 TTTATTTATTTCT-TA
1 TTTATTTATTTATCTA
*
630061 TTTATTAATTT
1 TTTATTTATTT
630072 TTTTTTTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTATTTATTTATCTA
Found at i:644579 original size:9 final size:9
Alignment explanation
Indices: 644565--644598 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
644555 GTATTGAGGC
644565 AGAAGAAAA
1 AGAAGAAAA
*
644574 AGAAGAGAA
1 AGAAGAAAA
*
644583 GGAAGAAAA
1 AGAAGAAAA
644592 AGAAGAA
1 AGAAGAA
644599 GACGTTGCCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (9 bp):
AGAAGAAAA
Found at i:653491 original size:20 final size:20
Alignment explanation
Indices: 653455--653498 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
653445 AATATACAAT
653455 ATAATAACAAAACAAATAAA
1 ATAATAACAAAACAAATAAA
*
653475 ATAATCACATAAA-AAATAAA
1 ATAATAACA-AAACAAATAAA
653495 ATAA
1 ATAA
653499 AATAACATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (20 bp):
ATAATAACAAAACAAATAAA
Found at i:653511 original size:25 final size:26
Alignment explanation
Indices: 653468--653519 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
653458 ATAACAAAAC
653468 AAATAAAATAATCACATAA-AAAATA
1 AAATAAAATAATCACATAATAAAATA
*
653493 AAATAAAATAA-CATTATAATAAAATA
1 AAATAAAATAATCA-CATAATAAAATA
653519 A
1 A
653520 CAATGCAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 2 0.08
25 15 0.62
26 7 0.29
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (26 bp):
AAATAAAATAATCACATAATAAAATA
Found at i:653529 original size:16 final size:16
Alignment explanation
Indices: 653489--653531 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
653479 TCACATAAAA
*
653489 AATAAAATAAAATAAC
1 AATACAATAAAATAAC
* *
653505 ATTATAATAAAATAAC
1 AATACAATAAAATAAC
*
653521 AATGCAATAAA
1 AATACAATAAA
653532 TAAAATGATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.23
Consensus pattern (16 bp):
AATACAATAAAATAAC
Found at i:653830 original size:27 final size:24
Alignment explanation
Indices: 653792--653862 Score: 79
Period size: 27 Copynumber: 2.8 Consensus size: 24
653782 GTGCAAAATC
653792 ATAAATGAAAAAAATAAAATAATAAA
1 ATAAAT-AAAAAAATAAAAT-ATAAA
*
653818 ATGAATATAAAAATAATAGAATATAAA
1 AT-AA-ATAAAAA-AATAAAATATAAA
*
653845 ATAAATACAAAAATAAAA
1 ATAAATAAAAAAATAAAA
653863 AAGGGTAGAC
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
24 6 0.15
25 6 0.15
26 4 0.10
27 14 0.36
28 9 0.23
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.21
Consensus pattern (24 bp):
ATAAATAAAAAAATAAAATATAAA
Found at i:653864 original size:8 final size:8
Alignment explanation
Indices: 653794--653864 Score: 52
Period size: 8 Copynumber: 8.2 Consensus size: 8
653784 GCAAAATCAT
653794 AAATGAAAA
1 AAAT-AAAA
653803 AAATAAAA
1 AAATAAAA
*
653811 TAATAAAA
1 AAATAAAA
* *
653819 TGAATATAA
1 -AAATAAAA
653828 AAATAATAGA
1 AAATAA-A-A
*
653838 ATATAAAA
1 AAATAAAA
*
653846 TAAATACAA
1 -AAATAAAA
653855 AAATAAAA
1 AAATAAAA
653863 AA
1 AA
653865 GGGTAGACCA
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
8 25 0.51
9 18 0.37
10 6 0.12
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (8 bp):
AAATAAAA
Found at i:654406 original size:26 final size:26
Alignment explanation
Indices: 654347--654406 Score: 95
Period size: 25 Copynumber: 2.3 Consensus size: 26
654337 TAAAAGTCAA
654347 TTTTTTTTAAAAAAAAAATTCATTTC
1 TTTTTTTTAAAAAAAAAATTCATTTC
*
654373 TTCTTTTT-AAAAAAAAATTCATTTC
1 TTTTTTTTAAAAAAAAAATTCATTTC
654398 TTTTCTTTT
1 TTTT-TTTT
654407 TTTTATCTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 20 0.65
26 11 0.35
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTTTTTTAAAAAAAAAATTCATTTC
Found at i:663605 original size:23 final size:20
Alignment explanation
Indices: 663562--663605 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 20
663552 GGAAAAGATT
*
663562 GGGAAGAGAGAAAAATAAAA
1 GGGAAGAGAAAAAAATAAAA
663582 GGGAAGAAGAAAAGAAATATAAA
1 GGGAAG-AGAAAA-AAATA-AAA
663605 G
1 G
663606 AAAAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 5 0.25
22 5 0.25
23 4 0.20
ACGTcount: A:0.64, C:0.00, G:0.30, T:0.07
Consensus pattern (20 bp):
GGGAAGAGAAAAAAATAAAA
Found at i:664548 original size:20 final size:19
Alignment explanation
Indices: 664520--664576 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 19
664510 GAGAAATTTT
*
664520 TTTTTGAATTTTTATATATA
1 TTTTAGAATTTTTATATA-A
664540 TTTTAGAATTTTTA-ATAA
1 TTTTAGAATTTTTATATAA
664558 TTTT--AATTTTT-TATAA
1 TTTTAGAATTTTTATATAA
664574 TTT
1 TTT
664577 GTTTTAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
16 14 0.40
18 5 0.14
19 3 0.09
20 13 0.37
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.65
Consensus pattern (19 bp):
TTTTAGAATTTTTATATAA
Found at i:668296 original size:45 final size:44
Alignment explanation
Indices: 668235--668321 Score: 129
Period size: 45 Copynumber: 2.0 Consensus size: 44
668225 TCGAAAGATC
* * * *
668235 GATATATTGTATTGGGAGTGATATACTGAACTGGCTCGTAAGAGT
1 GATATACTGTACTGGGAGCGATATACTGAA-TGACTCGTAAGAGT
668280 GATATACTGTACTGGGAGCGATATACTGAATGACTCGTAAGA
1 GATATACTGTACTGGGAGCGATATACTGAATGACTCGTAAGA
668322 TTGGCTTGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
44 11 0.29
45 27 0.71
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.30
Consensus pattern (44 bp):
GATATACTGTACTGGGAGCGATATACTGAATGACTCGTAAGAGT
Found at i:668437 original size:35 final size:36
Alignment explanation
Indices: 668370--668452 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 36
668360 TACTGACTGG
* * *
668370 GCTCGTACGAGCAAAATTTTACTGGGAGACTTGAAGA
1 GCTCGTATGAGCAAAA-TTTACTAGGAAACTTGAAGA
*
668407 GCTCGTATGAGCTAAA-TTACTAGGAAACTTGAAGA
1 GCTCGTATGAGCAAAATTTACTAGGAAACTTGAAGA
* *
668442 GATCGTTTGAG
1 GCTCGTATGAG
668453 ATAAGAATGT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
35 26 0.65
37 14 0.35
ACGTcount: A:0.33, C:0.14, G:0.27, T:0.27
Consensus pattern (36 bp):
GCTCGTATGAGCAAAATTTACTAGGAAACTTGAAGA
Found at i:670026 original size:25 final size:25
Alignment explanation
Indices: 669871--670034 Score: 179
Period size: 25 Copynumber: 6.6 Consensus size: 25
669861 TCTACTGAGC
* *
669871 CCAGACAGATTAACGCTC-TAGCGAG
1 CCAGACAGAATATCGCTCTTA-CGAG
* *
669896 CCAAACA-AATTATCGTTCTTACGAG
1 CCAGACAGAA-TATCGCTCTTACGAG
* *
669921 CCAGACAGAGTATCGCTCTTATGAG
1 CCAGACAGAATATCGCTCTTACGAG
* * *
669946 CCAGGCAGAGTATCGCTCTTATGAG
1 CCAGACAGAATATCGCTCTTACGAG
* * *
669971 CCAGGCAGAGTATCGCTCTTACAAG
1 CCAGACAGAATATCGCTCTTACGAG
*
669996 CTAGACAGAATATCGCTCTTACGAG
1 CCAGACAGAATATCGCTCTTACGAG
670021 CCAGACAGAATATC
1 CCAGACAGAATATC
670035 TTCATCGTCT
Statistics
Matches: 120, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
24 1 0.01
25 116 0.97
26 3 0.03
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (25 bp):
CCAGACAGAATATCGCTCTTACGAG
Found at i:670246 original size:20 final size:20
Alignment explanation
Indices: 670221--670258 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
670211 CTAAATCAAC
*
670221 AAATCATTAAATTCCAAATT
1 AAATCATGAAATTCCAAATT
*
670241 AAATCATGAAATTTCAAA
1 AAATCATGAAATTCCAAA
670259 AATTTCTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.13, G:0.03, T:0.32
Consensus pattern (20 bp):
AAATCATGAAATTCCAAATT
Found at i:676422 original size:25 final size:25
Alignment explanation
Indices: 676387--676437 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
676377 GTGTATTCAG
*
676387 TAAGCATTTAAAGGTTGTCAAGACA
1 TAAGCAGTTAAAGGTTGTCAAGACA
676412 TAAGCAGTTAAAGGTTGTCAAGACA
1 TAAGCAGTTAAAGGTTGTCAAGACA
676437 T
1 T
676438 CTCTGGATGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.27
Consensus pattern (25 bp):
TAAGCAGTTAAAGGTTGTCAAGACA
Found at i:677847 original size:18 final size:18
Alignment explanation
Indices: 677824--677870 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
677814 GTGGTGCTCC
*
677824 TCCTTGCGCTTCTTCTTA
1 TCCTTGTGCTTCTTCTTA
677842 TCCTTGTGCTTCTTCTTA
1 TCCTTGTGCTTCTTCTTA
677860 TCCTTGTGCTT
1 TCCTTGTGCTT
677871 GTGTTTTCGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.04, C:0.30, G:0.13, T:0.53
Consensus pattern (18 bp):
TCCTTGTGCTTCTTCTTA
Found at i:678188 original size:24 final size:24
Alignment explanation
Indices: 678138--678191 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
678128 GACAAAAAAT
* *
678138 TTCTTCCTTGTCTCCTTCTTTTCC
1 TTCTTCCTTGTCTCCTCCTTCTCC
*
678162 TTCTTCCTTTTCCTCCTCCTTCT-C
1 TTCTTCCTTGT-CTCCTCCTTCTCC
678186 TTCTTC
1 TTCTTC
678192 TTTCTCTTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 17 0.65
25 9 0.35
ACGTcount: A:0.00, C:0.41, G:0.02, T:0.57
Consensus pattern (24 bp):
TTCTTCCTTGTCTCCTCCTTCTCC
Found at i:685622 original size:17 final size:17
Alignment explanation
Indices: 685592--685632 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
685582 AAACTAAAAT
685592 GAATGCAACAACAATTAA
1 GAATGCAACAACAA-TAA
685610 -AATGCAAGC-ACAATAA
1 GAATGCAA-CAACAATAA
685626 GAATGCA
1 GAATGCA
685633 TGAAAACTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 3 0.14
17 17 0.81
18 1 0.05
ACGTcount: A:0.54, C:0.17, G:0.15, T:0.15
Consensus pattern (17 bp):
GAATGCAACAACAATAA
Found at i:686508 original size:47 final size:47
Alignment explanation
Indices: 686427--686519 Score: 150
Period size: 47 Copynumber: 2.0 Consensus size: 47
686417 GGAAATCTAG
* *
686427 CAGTGGGGTTTGGCTAATCTAGCTTAATGCAGCGGCAAGGGCTTCAA
1 CAGTAGGGTCTGGCTAATCTAGCTTAATGCAGCGGCAAGGGCTTCAA
* *
686474 CAGTAGGGTCTGGCTAATCTGGCTTAATGTAGCGGCAAGGGCTTCA
1 CAGTAGGGTCTGGCTAATCTAGCTTAATGCAGCGGCAAGGGCTTCA
686520 TTCCATGCCT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (47 bp):
CAGTAGGGTCTGGCTAATCTAGCTTAATGCAGCGGCAAGGGCTTCAA
Found at i:697625 original size:36 final size:36
Alignment explanation
Indices: 697578--697650 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
697568 AGGTTGAGGA
697578 AGATGGTGAAAATATGGTTTAGTTCATCAAATTCTT
1 AGATGGTGAAAATATGGTTTAGTTCATCAAATTCTT
697614 AGATGGTGAAAATATGGTTTAGTTCATCAAATTCTT
1 AGATGGTGAAAATATGGTTTAGTTCATCAAATTCTT
697650 A
1 A
697651 CTTAATGCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.38
Consensus pattern (36 bp):
AGATGGTGAAAATATGGTTTAGTTCATCAAATTCTT
Found at i:717162 original size:21 final size:21
Alignment explanation
Indices: 717138--717188 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
717128 GTGATACTTT
* *
717138 TACCGATACAAGTCATGCTTC
1 TACCGATACAAGCCATGCTAC
717159 TACCGATACAAGCCATGCTAC
1 TACCGATACAAGCCATGCTAC
*
717180 TCCCGATAC
1 TACCGATAC
717189 TAAAAACTCC
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:0.29, C:0.33, G:0.14, T:0.24
Consensus pattern (21 bp):
TACCGATACAAGCCATGCTAC
Found at i:717934 original size:43 final size:43
Alignment explanation
Indices: 717823--717947 Score: 146
Period size: 43 Copynumber: 2.9 Consensus size: 43
717813 TCTTTAAATT
* *
717823 AAACTTAATCTCATGCTTATTCTGAGTCACGAGTCTTCCTTTA
1 AAACATAATCTCATGCTTATTCTGAGTCATGAGTCTTCCTTTA
* * *
717866 AAACATAACCTCACT-CTCT-TTCTGAGTCATGAGACTTCCTTTT
1 AAACATAATCTCA-TGCT-TATTCTGAGTCATGAGTCTTCCTTTA
* * *
717909 TAACATAATCTCATGCTTATCCTGAGACATGAGTCTTCC
1 AAACATAATCTCATGCTTATTCTGAGTCATGAGTCTTCC
717948 ATCAATTTAC
Statistics
Matches: 68, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
42 2 0.03
43 64 0.94
44 2 0.03
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (43 bp):
AAACATAATCTCATGCTTATTCTGAGTCATGAGTCTTCCTTTA
Found at i:723329 original size:21 final size:21
Alignment explanation
Indices: 723305--723357 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
723295 ACTTGTGATA
*
723305 CTTCTACCGATATAAGTCATG
1 CTTCTACCGATACAAGTCATG
*
723326 CTTCTACCTATACAAGTCATG
1 CTTCTACCGATACAAGTCATG
* *
723347 CTACTATCGAT
1 CTTCTACCGAT
723358 GCTAAAACCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.34
Consensus pattern (21 bp):
CTTCTACCGATACAAGTCATG
Found at i:724143 original size:41 final size:41
Alignment explanation
Indices: 724097--724213 Score: 144
Period size: 41 Copynumber: 2.8 Consensus size: 41
724087 TTAACATAAT
* * *
724097 CTCATGCTTATCCCGAGACATAAATCTTTCTTTAATATCCC
1 CTCATGCTCATCCCGAGACATAAATCTTCCTTTAATATACC
** * *
724138 CTCATGCTCATCCTAAGACATGAGTCTTCCTTTAATATACC
1 CTCATGCTCATCCCGAGACATAAATCTTCCTTTAATATACC
* *
724179 CTCATGCTCATCCCGAGACATGAGTCTTCCATTTA
1 CTCATGCTCATCCCGAGACATAAATCTTCC-TTTA
724214 TACATAAAGA
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
41 62 0.94
42 4 0.06
ACGTcount: A:0.26, C:0.30, G:0.10, T:0.34
Consensus pattern (41 bp):
CTCATGCTCATCCCGAGACATAAATCTTCCTTTAATATACC
Found at i:731279 original size:49 final size:49
Alignment explanation
Indices: 731226--731333 Score: 164
Period size: 49 Copynumber: 2.2 Consensus size: 49
731216 TAATCATGGA
*
731226 ATACAGTCATCAATTTAGCACATAACATTTCATACATTTATATTGGCTT
1 ATACAATCATCAATTTAGCACATAACATTTCATACATTTATATTGGCTT
** *
731275 ATACAATCATCAATTTAGCATGTAACATTTCATACATTTATATTGAG-AT
1 ATACAATCATCAATTTAGCACATAACATTTCATACATTTATATTG-GCTT
731324 ATACAATCAT
1 ATACAATCAT
731334 GGCTTAATCA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
49 53 0.98
50 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.38
Consensus pattern (49 bp):
ATACAATCATCAATTTAGCACATAACATTTCATACATTTATATTGGCTT
Found at i:736503 original size:6 final size:6
Alignment explanation
Indices: 736487--736537 Score: 63
Period size: 6 Copynumber: 8.8 Consensus size: 6
736477 TAATTTATTG
*
736487 TTTTC- TTTTCT TTTTCT TTCTTCT TTTTCT TTTT-T TTTT-T TTTTGT
1 TTTTCT TTTTCT TTTTCT TT-TTCT TTTTCT TTTTCT TTTTCT TTTTCT
736533 TTTTC
1 TTTTC
736538 AAGTGACTGA
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
5 15 0.36
6 21 0.50
7 6 0.14
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:736512 original size:13 final size:12
Alignment explanation
Indices: 736487--736537 Score: 63
Period size: 11 Copynumber: 4.4 Consensus size: 12
736477 TAATTTATTG
736487 TTTTC-TTTTCT
1 TTTTCTTTTTCT
736498 TTTTCTTTCTTCT
1 TTTTCTTT-TTCT
736511 TTTTCTTTTT-T
1 TTTTCTTTTTCT
*
736522 TTTT-TTTTTGT
1 TTTTCTTTTTCT
736533 TTTTC
1 TTTTC
736538 AAGTGACTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
10 5 0.14
11 15 0.42
12 4 0.11
13 12 0.33
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (12 bp):
TTTTCTTTTTCT
Found at i:745661 original size:16 final size:16
Alignment explanation
Indices: 745640--745671 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
745630 GGTATTTTTT
*
745640 ATGTTAAAGGATTAAA
1 ATGTTAAAGGAATAAA
745656 ATGTTAAAGGAATAAA
1 ATGTTAAAGGAATAAA
745672 TTTATAAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (16 bp):
ATGTTAAAGGAATAAA
Found at i:746154 original size:24 final size:24
Alignment explanation
Indices: 746121--746190 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
746111 CGCTATTCTG
*
746121 ATTCTGGGCTCGTAAGAGCTAACC
1 ATTCTAGGCTCGTAAGAGCTAACC
*
746145 ATTCTAGGCTCGTGAGAGCTAACC
1 ATTCTAGGCTCGTAAGAGCTAACC
*
746169 -TATCTAGGCTCGTATGAGCTAA
1 AT-TCTAGGCTCGTAAGAGCTAA
746191 TTTTTTATGG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.02
24 40 0.98
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (24 bp):
ATTCTAGGCTCGTAAGAGCTAACC
Found at i:753403 original size:26 final size:26
Alignment explanation
Indices: 753359--753408 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
753349 CTTAAGCCAA
* * *
753359 ACTTTTCAAAAGTATTTTTTAAAATC
1 ACTTTTCAAAAGCACTTTTCAAAATC
*
753385 ACTTTTCCAAAGCACTTTTCAAAA
1 ACTTTTCAAAAGCACTTTTCAAAA
753409 ACAAAATTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.04, T:0.40
Consensus pattern (26 bp):
ACTTTTCAAAAGCACTTTTCAAAATC
Found at i:753932 original size:20 final size:22
Alignment explanation
Indices: 753902--753942 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
753892 TTTTTTTGTA
*
753902 AAAATATAAAATAA-ATATTTG
1 AAAATATAAAAGAATATATTTG
753923 AAAA-ATAAAAGAATATATTT
1 AAAATATAAAAGAATATATTT
753943 TATATTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (22 bp):
AAAATATAAAAGAATATATTTG
Found at i:754659 original size:18 final size:17
Alignment explanation
Indices: 754602--754660 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
754592 ATACGTGATG
* *
754602 AAAAATATTAAAAAGAT
1 AAAAATATAAAAAATAT
*
754619 AAAAATCAATAAAAATTAT
1 AAAAAT--ATAAAAAATAT
754638 -AAAATATAAACAAATAT
1 AAAAATATAAA-AAATAT
754655 AAAAAT
1 AAAAAT
754661 TAGATAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
16 5 0.15
17 11 0.32
18 10 0.29
19 8 0.24
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (17 bp):
AAAAATATAAAAAATAT
Found at i:755735 original size:80 final size:80
Alignment explanation
Indices: 755642--755801 Score: 320
Period size: 80 Copynumber: 2.0 Consensus size: 80
755632 ATTACTTTTA
755642 ATTTAATAATATTTAGAATATAATAATATGATAACTTTTAAAATATAATTTAAGATTATTTACCG
1 ATTTAATAATATTTAGAATATAATAATATGATAACTTTTAAAATATAATTTAAGATTATTTACCG
755707 TATATTGTTGGAATC
66 TATATTGTTGGAATC
755722 ATTTAATAATATTTAGAATATAATAATATGATAACTTTTAAAATATAATTTAAGATTATTTACCG
1 ATTTAATAATATTTAGAATATAATAATATGATAACTTTTAAAATATAATTTAAGATTATTTACCG
755787 TATATTGTTGGAATC
66 TATATTGTTGGAATC
755802 TTCTCAACAT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (80 bp):
ATTTAATAATATTTAGAATATAATAATATGATAACTTTTAAAATATAATTTAAGATTATTTACCG
TATATTGTTGGAATC
Found at i:756145 original size:22 final size:23
Alignment explanation
Indices: 756120--756171 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
756110 GAATTAAATA
*
756120 ATAAATATTAGTTTT-TTATTAT
1 ATAAATATTAGTTTTATTAGTAT
756142 ATAAATATTAGTTTTAATTAGTAT
1 ATAAATATTAGTTTT-ATTAGTAT
756166 ATAAAT
1 ATAAAT
756172 GTAACATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 15 0.56
24 12 0.44
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (23 bp):
ATAAATATTAGTTTTATTAGTAT
Found at i:756726 original size:20 final size:21
Alignment explanation
Indices: 756699--756748 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
756689 TAAAAAAATA
756699 TATAAAAAATTATAGAA-ATT
1 TATAAAAAATTATAGAATATT
*
756719 TATTAAAAA-TATAGAATATT
1 TATAAAAAATTATAGAATATT
756739 TATAAAAAAT
1 TATAAAAAAT
756749 CATTAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (21 bp):
TATAAAAAATTATAGAATATT
Found at i:757255 original size:18 final size:18
Alignment explanation
Indices: 757232--757271 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
757222 GATTTTCTAT
757232 ATAATTTTCTAACTTTTA
1 ATAATTTTCTAACTTTTA
* *
757250 ATAATTTTGTAATTTTTA
1 ATAATTTTCTAACTTTTA
757268 ATAA
1 ATAA
757272 AATTTAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (18 bp):
ATAATTTTCTAACTTTTA
Done.