Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009496.1 Kokia drynarioides strain JFW-HI SEQ_124206, 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: 7170
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Found at i:1321 original size:48 final size:48
Alignment explanation
Indices: 1255--1378 Score: 205
Period size: 48 Copynumber: 2.6 Consensus size: 48
1245 TTAAGTGTTT
* *
1255 TTTTTTTTGTTAAATGCATCTTTGTTTAATAATCTGCATCATTAAGTG
1 TTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTGCATCATTAACTG
* *
1303 TTTTGTTTGTTAAATGCATCTTTGTTTAGTAATCTGCATTATTAACTG
1 TTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTGCATCATTAACTG
1351 TTTTGTTTGTTAAATGCATCTTT-TTTAA
1 TTTTGTTTGTTAAATGCATCTTTGTTTAA
1379 ATGCCTTGCA
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
47 4 0.06
48 67 0.94
ACGTcount: A:0.23, C:0.10, G:0.13, T:0.54
Consensus pattern (48 bp):
TTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTGCATCATTAACTG
Found at i:1912 original size:75 final size:76
Alignment explanation
Indices: 1819--1963 Score: 202
Period size: 80 Copynumber: 1.9 Consensus size: 76
1809 GGAGAAATGT
* * * *
1819 CATGCCTTTTCAGCTACATCAGATCC-AAGAGACATGACTCATTGGCTTTCCTACAAGTGTTAAA
1 CATGCCTTTTCAACTACATCAGATCCAAAGAGACATGACTCATTAGCTTCCCTACAAGAGTTAAA
1883 AACGAAATTGC
66 AACGAAATTGC
*
1894 CATGCCTTTTTAACTACATCAGATCCTAATGAAGAGACATGACTCATTAGCTTCCCTACAAGAGT
1 CATGCCTTTTCAACTACATCAGATCC--A--AAGAGACATGACTCATTAGCTTCCCTACAAGAGT
1959 TAAAA
62 TAAAA
1964 TGAAATTAGT
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
75 24 0.40
80 36 0.60
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.28
Consensus pattern (76 bp):
CATGCCTTTTCAACTACATCAGATCCAAAGAGACATGACTCATTAGCTTCCCTACAAGAGTTAAA
AACGAAATTGC
Found at i:2854 original size:216 final size:216
Alignment explanation
Indices: 2394--4378 Score: 2286
Period size: 216 Copynumber: 9.3 Consensus size: 216
2384 AGTGACTTGT
* * * * *
2394 AATTGGTCGAAGGAATGGATCATCTTGAATACTCTCAAGAACTGAAGTTATAAAAGAACTCGTAA
1 AATTGGTCAAAGGAATGGATCGTCTTGAATACTCTCAGGAACCGAAGTTATAAAAGAACTAGTAA
* ** * * * *
2459 AGGTTTGACAAGTTTAGAAGTTCGTCCAAGAA-CTAGAGAGAAACAATTCACATGTAAATAAGTT
66 ATGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTT
* * *
2523 TTTAATTCAAAGATCAAAAGTTGTTTCCAAAATGAC-AACTATTAAGACCAAATGATGCGATTTC
131 TTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTC
* *
2587 TCGACCACGGAATGTTCGAAA
196 TCGATCATGGAATGTTCGAAA
* * * * *
2608 AATTGGTCAATGGAATGGATCGTCTTGAATACTATCAGGAATCGACGTAATAAAAGAACTAGTAA
1 AATTGGTCAAAGGAATGGATCGTCTTGAATACTCTCAGGAACCGAAGTTATAAAAGAACTAGTAA
*
2673 ATGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAAGAATTCTCACGTAAAAAAGTT
66 ATGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTT
* * * * * * *
2738 TTTAATTTAAAGACCAAAAGTTATTTACAAAATGGCAAATTATTTTGACCAAATGATGTGATTTT
131 TTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTC
* *
2803 TCAATCATGGAATCTTCGAAA
196 TCGATCATGGAATGTTCGAAA
* * * *
2824 AATTGGTCAAAGGAATGGATCGCCTTGAATACTCTTAGAAATCGAAGTTATAAAAGAACTAGTAA
1 AATTGGTCAAAGGAATGGATCGTCTTGAATACTCTCAGGAACCGAAGTTATAAAAGAACTAGTAA
* * * *
2889 ATGTTTAACAAATTCGGAAGTTCGTCCAAGAACCAAGAGAGAAGCAATTCTCTCGTAAAAAAGTT
66 ATGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTT
* * * *
2954 TTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTTTTTTGTCCAAATGATGCTATTTC
131 TTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTC
*
3019 TCGAGCATGGAATGTTC-AGAA
196 TCGATCATGGAATGTTCGA-AA
* * * * * *
3040 AATTGGTCGAAGGAATAGATCATCTTGAATACTCTCGGGAACCAAAGTTATAAAAGAACTCGTAA
1 AATTGGTCAAAGGAATGGATCGTCTTGAATACTCTCAGGAACCGAAGTTATAAAAGAACTAGTAA
* * * * *
3105 AGGTTTGACAAGTTCAGAAGTTCATCCAAGAA-CAAGAGAGAAACAATTCACACGTAAATAAGTT
66 ATGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTT
* * * *
3169 TTTAATTCAAAGACCAAAATTTGTTTCCAAAATGAC-AACTATTAAGACCAAATGATGCAATTTC
131 TTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTC
3233 TCGATCATGGAATGTTCGAAA
196 TCGATCATGGAATGTTCGAAA
* * * * * *
3254 AATTGGTCAAGGGAATGGATCGTCTTGACTACTATCAGGAATCGACGTAATAAAAGAACTAGTAA
1 AATTGGTCAAAGGAATGGATCGTCTTGAATACTCTCAGGAACCGAAGTTATAAAAGAACTAGTAA
* * *
3319 ATGTTTGACAAGCTCGGAAGTTCGTCCAAGAACCAAGAGAGAAAGAATTCTCACATAAAAAAGTT
66 ATGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTT
* *
3384 TTTAATTTAAAGACCAAAAGTTATTTACAAAATTG-CAAACTATTTTA-ACCAAATGATGCGATT
131 TTTAATTCAAAGACCAAAAGTTGTTTACAAAA-TGACAAACTA-TTTAGACCAAATGATGCGATT
* * * *
3447 TTTCCATCATGGAATATTCGGAA
194 TCTCGATCATGGAATGTTCGAAA
* * *
3470 AATTGGTCAAAGGAATGGATTGTCTTGAATACTCTCAGGAACAGAAGTTATAAAAGAACTTGTAA
1 AATTGGTCAAAGGAATGGATCGTCTTGAATACTCTCAGGAACCGAAGTTATAAAAGAACTAGTAA
* * * * * * * *
3535 AAGTTTGACAAGTTCGTATGTTCATCCAAGAACCAAGA-AGGAAACAACTCTCATGGAAATAAGT
66 ATGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGA-GAAACAATTCTCACGTAAAAAAGT
* * * *
3599 ATTTAATTCAAAGACCAAAAGTTGTTTAAAAAATGACAAACTATTTAGATCAAATGAAGCGATTT
130 TTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT
* ** *
3664 CCCGGGCATGGAATGTTCAAAA
195 CTCGATCATGGAATGTTCGAAA
* * * * * *
3686 AAATGGTCGAAA-GAATTGATCATCTTTAATACACTTAGGAACCGAAGTTATAAAAGAACTCA-T
1 AATTGGTC-AAAGGAATGGATCGTCTTGAATACTCTCAGGAACCGAAGTTATAAAAGAACT-AGT
* ** * * * * * *
3749 AAATGTTTCATGAGTTCAGAAGTTCATCAAAGAACTAATAGAGAAACAATTCTCACGTAAAATAG
64 AAATGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAG
*
3814 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGATCAAATGATGCGATT
129 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATT
* * *
3879 TCTC-AGCATGGAATTTTAG-AA
194 TCTCGATCATGGAATGTTCGAAA
* * * * * * * *
3900 AATTGCTCAAATGAAAGGATCGTCTTGAATACTTTAAGGAATCGAAGTTATGAAAGAACTTGTAA
1 AATTGGTCAAAGGAATGGATCGTCTTGAATACTCTCAGGAACCGAAGTTATAAAAGAACTAGT-A
* * * * * * * *
3965 AAT-TTTGACTACTTTGTATGTTAGTCCATGAACCAAGA-AGGAAACAATACTCACGTAAAAAAG
65 AATGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGA-GAAACAATTCTCACGTAAAAAAG
* * * *
4028 TATTTAGTTCAAAG-CACAAAAGTTGTTTACAAAAT-AGCAAATTATTAAGACCAAATGATGCGA
129 TTTTTAATTCAAAGAC-CAAAAGTTGTTTACAAAATGA-CAAACTATTTAGACCAAATGATGCGA
* * *
4091 ATTCCCGATCATGGAATGTTCAAAA
192 TTTCTCGATCATGGAATGTTCGAAA
* * * * *
4116 AATTGGTCGAATGAATGGATCGTCTTGACTACTATCAGGAGCCGAAGTTATAAAAGAACTAGTAA
1 AATTGGTCAAAGGAATGGATCGTCTTGAATACTCTCAGGAACCGAAGTTATAAAAGAACTAGTAA
* *
4181 ATGTTTGACAAGTTCGGATGTTCGTCTAAGAA-CAAGA-AG-AA-AA-----A-G---AAAA-TT
66 ATGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTT
* *
4232 TTTAATTCAAAAGACCAAAAGTTATTTACAAAATGACAAACTATTCT-GACCAAATAATGCGATT
131 TTTAATTC-AAAGACCAAAAGTTGTTTACAAAATGACAAACTATT-TAGACCAAATGATGCGATT
* * *
4296 TCCCGATCATGGAATCTTCTAAA
194 TCTCGATCATGGAATGTTCGAAA
* * *
4319 AATTAGTCAAAGGAATGGATCGTCTTGGATACTCTTAGGAACCGAAGTTATAAAAGAACT
1 AATTGGTCAAAGGAATGGATCGTCTTGAATACTCTCAGGAACCGAAGTTATAAAAGAACT
4379 CGTTGATACG
Statistics
Matches: 1492, Mismatches: 252, Indels: 65
0.82 0.14 0.04
Matches are distributed among these distances:
202 8 0.01
203 122 0.08
204 2 0.00
206 1 0.00
207 1 0.00
212 2 0.00
213 8 0.01
214 355 0.24
215 222 0.15
216 764 0.51
217 7 0.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Consensus pattern (216 bp):
AATTGGTCAAAGGAATGGATCGTCTTGAATACTCTCAGGAACCGAAGTTATAAAAGAACTAGTAA
ATGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTT
TTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTC
TCGATCATGGAATGTTCGAAA
Found at i:3256 original size:430 final size:432
Alignment explanation
Indices: 2394--4381 Score: 2287
Period size: 430 Copynumber: 4.6 Consensus size: 432
2384 AGTGACTTGT
* * * *
2394 AATTGGTCGAAGGAATGGATCATCTTGAATACTCTCAAGAA-CTGAAGTTATAAAAGAACTCGTA
1 AATTGGTCAAAGGAATGGATCGTCTTGAATACTCTCAGGAATC-GAAGTTATAAAAGAACTAGTA
* ** * * * *
2458 AAGGTTTGACAAGTTTAGAAGTTCGTCCAAGAA-CTAGAGAGAAACAATTCACATGTAAATAAGT
65 AATGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGT
* * **
2522 TTTTAATTCAAAGATCAAAAGTTGTTTCCAAAATGAC-AACTATTAAGACCAAATGATGCGATTT
130 TTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTTGACCAAATGATGCGATTT
* * * * *
2586 CTCGACCACGGAATGTTC-GAAAAATTGGTCAATGGAATGGATCGTCTTGAATACTATCAGGAAT
195 CTCGAGCATGGAATGTTCAG-AAAATTGGTCAAAGGAATGGATCGTCTTGAATACTCTCAGGAAC
* * * * * *
2650 CGACGTAATAAAAGAACTAGTAAATGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAG-AGAG
259 CGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGTAAGTTCATCCAAGAACCAAGAAG-G
* * * * * *
2714 AAAGAATTCTCACGTAAAAAAGTTTTTAATTTAAAGACCAAAAGTTATTTACAAAATGGCAAATT
323 AAACAATTCTCACGTAAAAAAGTATTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACT
** ** ** * * *
2779 ATTTTGACCAAATGATGTGATTTTTCAATCATGGAATCTTCGAAA
388 ATTAAGACCAAATGATGCAATTTCCCGATCATGGAATGTTCAAAA
* * *
2824 AATTGGTCAAAGGAATGGATCGCCTTGAATACTCTTAGAAATCGAAGTTATAAAAGAACTAGTAA
1 AATTGGTCAAAGGAATGGATCGTCTTGAATACTCTCAGGAATCGAAGTTATAAAAGAACTAGTAA
* * * *
2889 ATGTTTAACAAATTCGGAAGTTCGTCCAAGAACCAAGAGAGAAGCAATTCTCTCGTAAAAAAGTT
66 ATGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTT
* * *
2954 TTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTTTTTTGTCCAAATGATGCTATTTC
131 TTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTTGACCAAATGATGCGATTTC
* * * * *
3019 TCGAGCATGGAATGTTCAGAAAATTGGTCGAAGGAATAGATCATCTTGAATACTCTCGGGAACCA
196 TCGAGCATGGAATGTTCAGAAAATTGGTCAAAGGAATGGATCGTCTTGAATACTCTCAGGAACCG
*
3084 AAGTTATAAAAGAACTCGTAAAGGTTTGACAAGTTCAG-AAGTTCATCCAAGAA-CAAG-AGAGA
261 AAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTC-GTAAGTTCATCCAAGAACCAAGAAG-GA
* * * * *
3146 AACAATTCACACGTAAATAAGTTTTTAATTCAAAGACCAAAATTTGTTTCCAAAATGAC-AACTA
324 AACAATTCTCACGTAAAAAAGTATTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTA
* *
3210 TTAAGACCAAATGATGCAATTTCTCGATCATGGAATGTTCGAAA
389 TTAAGACCAAATGATGCAATTTCCCGATCATGGAATGTTCAAAA
* * * * *
3254 AATTGGTCAAGGGAATGGATCGTCTTGACTACTATCAGGAATCGACGTAATAAAAGAACTAGTAA
1 AATTGGTCAAAGGAATGGATCGTCTTGAATACTCTCAGGAATCGAAGTTATAAAAGAACTAGTAA
* * *
3319 ATGTTTGACAAGCTCGGAAGTTCGTCCAAGAACCAAGAGAGAAAGAATTCTCACATAAAAAAGTT
66 ATGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTT
* * *
3384 TTTAATTTAAAGACCAAAAGTTATTTACAAAATTG-CAAACTATTTTAACCAAATGATGCGATTT
131 TTTAATTCAAAGACCAAAAGTTGTTTACAAAA-TGACAAACTATTTTGACCAAATGATGCGATTT
* * * * * * *
3448 TTCCATCATGGAATATTCGGAAAATTGGTCAAAGGAATGGATTGTCTTGAATACTCTCAGGAACA
195 CTCGAGCATGGAATGTTCAGAAAATTGGTCAAAGGAATGGATCGTCTTGAATACTCTCAGGAACC
* *
3513 GAAGTTATAAAAGAACTTGTAAAAGTTTGACAAGTTCGTATGTTCATCCAAGAACCAAGAAGGAA
260 GAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGTAAGTTCATCCAAGAACCAAGAAGGAA
* * * * *
3578 ACAACTCTCATGGAAATAAGTATTTAATTCAAAGACCAAAAGTTGTTTAAAAAATGACAAACTAT
325 ACAATTCTCACGTAAAAAAGTATTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTAT
* * * * **
3643 TTAGATCAAATGAAGCGATTTCCCGGGCATGGAATGTTCAAAA
390 TAAGACCAAATGATGCAATTTCCCGATCATGGAATGTTCAAAA
* * * * * * *
3686 AAATGGTCGAAA-GAATTGATCATCTTTAATACACTTAGGAACCGAAGTTATAAAAGAACTCA-T
1 AATTGGTC-AAAGGAATGGATCGTCTTGAATACTCTCAGGAATCGAAGTTATAAAAGAACT-AGT
* ** * * * * * *
3749 AAATGTTTCATGAGTTCAGAAGTTCATCAAAGAACTAATAGAGAAACAATTCTCACGTAAAATAG
64 AAATGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAG
* *
3814 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGATCAAATGATGCGATT
129 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTTGACCAAATGATGCGATT
* * * * * * *
3879 TCTC-AGCATGGAAT-TTTAGAAAATTGCTCAAATGAAAGGATCGTCTTGAATACTTTAAGGAAT
194 TCTCGAGCATGGAATGTTCAGAAAATTGGTCAAAGGAATGGATCGTCTTGAATACTCTCAGGAAC
* * * * * * * *
3942 CGAAGTTATGAAAGAACTTGTAAAATTTTGACTACTTTGTATGTT-AGTCCATGAACCAAGAAGG
259 CGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGTAAGTTCA-TCCAAGAACCAAGAAGG
* *
4006 AAACAATACTCACGTAAAAAAGTATTTAGTTCAAAG-CACAAAAGTTGTTTACAAAAT-AGCAAA
323 AAACAATTCTCACGTAAAAAAGTATTTAATTCAAAGAC-CAAAAGTTGTTTACAAAATGA-CAAA
*
4069 TTATTAAGACCAAATGATGCGAA-TTCCCGATCATGGAATGTTCAAAA
386 CTATTAAGACCAAATGATGC-AATTTCCCGATCATGGAATGTTCAAAA
* * * * **
4116 AATTGGTCGAATGAATGGATCGTCTTGACTACTATCAGGAGCCGAAGTTATAAAAGAACTAGTAA
1 AATTGGTCAAAGGAATGGATCGTCTTGAATACTCTCAGGAATCGAAGTTATAAAAGAACTAGTAA
* *
4181 ATGTTTGACAAGTTCGGATGTTCGTCTAAGAA-CAAGA-AG-AA-AA-----A-G---AAAA-TT
66 ATGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTT
* * *
4232 TTTAATTCAAAAGACCAAAAGTTATTTACAAAATGACAAACTATTCTGACCAAATAATGCGATTT
131 TTTAATTC-AAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTTGACCAAATGATGCGATTT
* * * * * *
4297 CCCGATCATGGAATCTTCTA-AAAATTAGTCAAAGGAATGGATCGTCTTGGATACTCTTAGGAAC
195 CTCGAGCATGGAATGTTC-AGAAAATTGGTCAAAGGAATGGATCGTCTTGAATACTCTCAGGAAC
4361 CGAAGTTATAAAAGAACTCGT
259 CGAAGTTATAAAAGAACTCGT
4382 TGATACGAGT
Statistics
Matches: 1328, Mismatches: 207, Indels: 57
0.83 0.13 0.04
Matches are distributed among these distances:
416 10 0.01
417 56 0.04
418 9 0.01
419 57 0.04
420 2 0.00
421 1 0.00
426 2 0.00
427 2 0.00
428 2 0.00
429 10 0.01
430 656 0.49
431 192 0.14
432 324 0.24
433 5 0.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Consensus pattern (432 bp):
AATTGGTCAAAGGAATGGATCGTCTTGAATACTCTCAGGAATCGAAGTTATAAAAGAACTAGTAA
ATGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTT
TTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTTGACCAAATGATGCGATTTC
TCGAGCATGGAATGTTCAGAAAATTGGTCAAAGGAATGGATCGTCTTGAATACTCTCAGGAACCG
AAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGTAAGTTCATCCAAGAACCAAGAAGGAAA
CAATTCTCACGTAAAAAAGTATTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATT
AAGACCAAATGATGCAATTTCCCGATCATGGAATGTTCAAAA
Found at i:3624 original size:646 final size:642
Alignment explanation
Indices: 2394--4381 Score: 2602
Period size: 646 Copynumber: 3.1 Consensus size: 642
2384 AGTGACTTGT
* *
2394 AATTGGTCGAAGGAATGGATCATCTTGAATACTCTCAAGAACTGAAGTTATAAAAGAACTCGTAA
1 AATTGGTCGAAGGAATGGATCATCTTGAATACTCTCAGGAACCGAAGTTATAAAAGAACTCGTAA
* * * *
2459 AGGTTTGACAAGTTTAGAAGTTCGTCCAAGAACTAGAGAGAAACAATTCACATGTAAATAAGTTT
66 AGGTTTGACAAGTTCAGAAGTTCATCCAAGAACAAGAGAGAAACAATTCACACGTAAATAAGTTT
*
2524 TTAATTCAAAGATCAAAAGTTGTTTCCAAAATGACAACTATTAAGACCAAATGATGCGATTTCTC
131 TTAATTCAAAGACCAAAAGTTGTTTCCAAAATGACAACTATTAAGACCAAATGATGCGATTTCTC
* *
2589 GACCACGGAATGTTCGAAAAATTGGTCAATGGAATGGATCGTCTTGAATACTATCAGGAATCGAC
196 GACCATGGAATGTTCGAAAAATTGGTCAAAGGAATGGATCGTCTTGAATACTATCAGGAATCGAC
*
2654 GTAATAAAAGAACTAGTAAATGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAAGA
261 GTAATAAAAGAACTAGTAAATGTTTGACAAGCTCGGAAGTTCGTCCAAGAACCAAGAGAGAAAGA
*
2719 ATTCTCACGTAAAAAAGTTTTTAATTTAAAGACCAAAAGTTATTTACAAAATGGCAAATTATTTT
326 ATTCTCACGTAAAAAAGTTTTTAATTTAAAGACCAAAAGTTATTTACAAAATAGCAAATTATTTT
* * * * *
2784 GACCAAATGATGTGATTTTTCAATCATGGAATCTTCGAAAAATTGGTCAAAGGAATGGATCGCCT
391 AACCAAATGATGCGATTTTTCCATCATGGAATATTCGAAAAATTGGTCAAAGGAATGGATCGTCT
* * * * *
2849 TGAATACTCTTAGAAATCGAAGTTATAAAAGAACTAGTAAATGTTTAACAAATTCGGAAGTTCGT
456 TGAATACTCTCAGGAA-CGAAGTTATAAAAGAACTAGTAAATGTTTGACAAGTTCGGATGTTCGT
* *
2914 CCAAGAACCAAG-AGAGAAGCAATTCTC-TCGTAAAAAAGTTTTTAATTCAAAGACCAAAAGTTG
520 CCAAGAACCAAGAAG-GAAACAA-TCTCAT-G-GAAAAAGTTTTTAATTCAAAGACCAAAAGTTG
* * *
2977 TTTACAAAATGACAAACTTTTTTGTCCAAATGATGCTATTTCTCGAGCATGGAATGTTCAGAA
581 TTTACAAAATGACAAACTATTTTGTCCAAATGATGCGATTTCCCGAGCATGGAATGTTCA-AA
* * *
3040 AATTGGTCGAAGGAATAGATCATCTTGAATACTCTCGGGAACCAAAGTTATAAAAGAACTCGTAA
1 AATTGGTCGAAGGAATGGATCATCTTGAATACTCTCAGGAACCGAAGTTATAAAAGAACTCGTAA
3105 AGGTTTGACAAGTTCAGAAGTTCATCCAAGAACAAGAGAGAAACAATTCACACGTAAATAAGTTT
66 AGGTTTGACAAGTTCAGAAGTTCATCCAAGAACAAGAGAGAAACAATTCACACGTAAATAAGTTT
* *
3170 TTAATTCAAAGACCAAAATTTGTTTCCAAAATGACAACTATTAAGACCAAATGATGCAATTTCTC
131 TTAATTCAAAGACCAAAAGTTGTTTCCAAAATGACAACTATTAAGACCAAATGATGCGATTTCTC
* * *
3235 GATCATGGAATGTTCGAAAAATTGGTCAAGGGAATGGATCGTCTTGACTACTATCAGGAATCGAC
196 GACCATGGAATGTTCGAAAAATTGGTCAAAGGAATGGATCGTCTTGAATACTATCAGGAATCGAC
3300 GTAATAAAAGAACTAGTAAATGTTTGACAAGCTCGGAAGTTCGTCCAAGAACCAAGAGAGAAAGA
261 GTAATAAAAGAACTAGTAAATGTTTGACAAGCTCGGAAGTTCGTCCAAGAACCAAGAGAGAAAGA
* * *
3365 ATTCTCACATAAAAAAGTTTTTAATTTAAAGACCAAAAGTTATTTACAAAATTGCAAACTATTTT
326 ATTCTCACGTAAAAAAGTTTTTAATTTAAAGACCAAAAGTTATTTACAAAATAGCAAATTATTTT
* *
3430 AACCAAATGATGCGATTTTTCCATCATGGAATATTCGGAAAATTGGTCAAAGGAATGGATTGTCT
391 AACCAAATGATGCGATTTTTCCATCATGGAATATTCGAAAAATTGGTCAAAGGAATGGATCGTCT
* * * *
3495 TGAATACTCTCAGGAACAGAAGTTATAAAAGAACTTGTAAAAGTTTGACAAGTTCGTATGTTCAT
456 TGAATACTCTCAGGAAC-GAAGTTATAAAAGAACTAGTAAATGTTTGACAAGTTCGGATGTTCGT
*
3560 CCAAGAACCAAGAAGGAAACAACTCTCATGGAAATAAGTATTTAATTCAAAGACCAAAAGTTGTT
520 CCAAGAACCAAGAAGGAAACAA-TCTCATGGAAA-AAGTTTTTAATTCAAAGACCAAAAGTTGTT
* * * *
3625 TAAAAAATGACAAACTATTTAGAT-CAAATGAAGCGATTTCCCGGGCATGGAATGTTCAAAA
583 TACAAAATGACAAACTATTTTG-TCCAAATGATGCGATTTCCCGAGCATGGAATGTTC-AAA
* * * * * * *
3686 AAATGGTCGAAAGAATTGATCATCTTTAATACACTTAGGAACCGAAGTTATAAAAGAACTCATAA
1 AATTGGTCGAAGGAATGGATCATCTTGAATACTCTCAGGAACCGAAGTTATAAAAGAACTCGTAA
* * ** * * *
3751 ATGTTTCATGAGTTCAGAAGTTCATCAAAGAACTAATAGAGAAACAATTCTCACGTAAA-ATAGT
66 AGGTTTGACAAGTTCAGAAGTTCATCCAAGAAC-AAGAGAGAAACAATTCACACGTAAATA-AGT
* * *
3815 TTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGATCAAATGATGCGATTT
129 TTTTAATTCAAAGACCAAAAGTTGTTTCCAAAATGAC-AACTATTAAGACCAAATGATGCGATTT
* * * * * * * *
3880 CTC-AGCATGGAATTTTAG-AAAATTGCTCAAATGAAAGGATCGTCTTGAATACTTTAAGGAATC
193 CTCGACCATGGAATGTTCGAAAAATTGGTCAAAGGAATGGATCGTCTTGAATACTATCAGGAATC
* * * * * * * * * *
3943 GAAGTTATGAAAGAACTTGTAAAAT-TTTGACTA-CTTTGTATGTTAGTCCATGAACCAAGA-AG
258 GACGTAATAAAAGAACTAGT-AAATGTTTGACAAGC-TCGGAAGTTCGTCCAAGAACCAAGAGA-
* * * * * *
4005 GAAACAATACTCACGTAAAAAAGTATTTAGTTCAAAG-CACAAAAGTTGTTTACAAAATAGCAAA
320 GAAAGAATTCTCACGTAAAAAAGTTTTTAATTTAAAGAC-CAAAAGTTATTTACAAAATAGCAAA
* * * * * * *
4069 TTA-TTAAGACCAAATGATGCGA-ATTCCCGATCATGGAATGTTCAAAAAATTGGTCGAATGAAT
384 TTATTTTA-ACCAAATGATGCGATTTTTCC-ATCATGGAATATTCGAAAAATTGGTCAAAGGAAT
* * *
4132 GGATCGTCTTGACTACTATCAGGAGCCGAAGTTATAAAAGAACTAGTAAATGTTTGACAAGTTCG
447 GGATCGTCTTGAATACTCTCAGGA-ACGAAGTTATAAAAGAACTAGTAAATGTTTGACAAGTTCG
*
4197 GATGTTCGTCTAAGAA-CAAGAA-G-AA-AA----A--G-AAAA-TTTTTAATTCAAAAGACCAA
511 GATGTTCGTCCAAGAACCAAGAAGGAAACAATCTCATGGAAAAAGTTTTTAATTC-AAAGACCAA
* * * * * *
4250 AAGTTATTTACAAAATGACAAACTATTCTGACCAAATAATGCGATTTCCCGATCATGGAATCTTC
575 AAGTTGTTTACAAAATGACAAACTATTTTGTCCAAATGATGCGATTTCCCGAGCATGGAATGTTC
4315 TAAA
640 -AAA
* * * * *
4319 AATTAGTCAAAGGAATGGATCGTCTTGGATACTCTTAGGAACCGAAGTTATAAAAGAACTCGT
1 AATTGGTCGAAGGAATGGATCATCTTGAATACTCTCAGGAACCGAAGTTATAAAAGAACTCGT
4382 TGATACGAGT
Statistics
Matches: 1188, Mismatches: 136, Indels: 49
0.87 0.10 0.04
Matches are distributed among these distances:
632 9 0.01
633 121 0.10
634 2 0.00
635 1 0.00
637 1 0.00
642 2 0.00
643 2 0.00
644 1 0.00
645 20 0.02
646 919 0.77
647 83 0.07
648 27 0.02
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Consensus pattern (642 bp):
AATTGGTCGAAGGAATGGATCATCTTGAATACTCTCAGGAACCGAAGTTATAAAAGAACTCGTAA
AGGTTTGACAAGTTCAGAAGTTCATCCAAGAACAAGAGAGAAACAATTCACACGTAAATAAGTTT
TTAATTCAAAGACCAAAAGTTGTTTCCAAAATGACAACTATTAAGACCAAATGATGCGATTTCTC
GACCATGGAATGTTCGAAAAATTGGTCAAAGGAATGGATCGTCTTGAATACTATCAGGAATCGAC
GTAATAAAAGAACTAGTAAATGTTTGACAAGCTCGGAAGTTCGTCCAAGAACCAAGAGAGAAAGA
ATTCTCACGTAAAAAAGTTTTTAATTTAAAGACCAAAAGTTATTTACAAAATAGCAAATTATTTT
AACCAAATGATGCGATTTTTCCATCATGGAATATTCGAAAAATTGGTCAAAGGAATGGATCGTCT
TGAATACTCTCAGGAACGAAGTTATAAAAGAACTAGTAAATGTTTGACAAGTTCGGATGTTCGTC
CAAGAACCAAGAAGGAAACAATCTCATGGAAAAAGTTTTTAATTCAAAGACCAAAAGTTGTTTAC
AAAATGACAAACTATTTTGTCCAAATGATGCGATTTCCCGAGCATGGAATGTTCAAA
Found at i:6178 original size:17 final size:19
Alignment explanation
Indices: 6136--6181 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
6126 TCAAAAAGTC
6136 GAGAAAAA-AAGAAAAATAT
1 GAGAAAAATAA-AAAAATAT
6155 GAGAAAAATAAAAAAATAT
1 GAGAAAAATAAAAAAATAT
6174 -A-AAAAATA
1 GAGAAAAATA
6182 TTTTATGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.27
18 1 0.04
19 16 0.62
20 2 0.08
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (19 bp):
GAGAAAAATAAAAAAATAT
Done.