Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013209.1 Kokia drynarioides strain JFW-HI SEQ_128228, 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: 8628
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Found at i:5940 original size:216 final size:216
Alignment explanation
Indices: 5552--6153 Score: 699
Period size: 216 Copynumber: 2.8 Consensus size: 216
5542 TGATTGTTTG
* * ** * * * * * *
5552 AATGAAAAACTATTTAGACTAAATGATATGATTTCCC-GAGAATGGATTGTTCGGAAAACTGCTC
1 AATGAAAAACTATTTAGACCAAATAATGCGATTTCCCTCA-CATGGAATGTTCGCAAAATTACTC
* * ** * ** * * *
5616 GAAGGAATGGACCGTCTTGATTACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTCGA
65 GAACGAATGGATCGTCTTGAACACTTTAATGAACATAAGCTATAAAAGAACTCGTAAAAGTTTGT
* * * * * * *
5681 CTAGTTCGGAAGTTCATCCAAGAACAAAGAGAGACATAATTCTCATGTAAATAAAATTTTAATTC
130 CAATTTCAGAATTTCGTCCAAGAACAAAGAGAGAAACAATTCTCATGTAAATAAAATTTTAATTC
* **
5746 AAAGATCAAATTTTGTTTACAA
195 AAAGATAAAAACTTGTTTACAA
* **
5768 AATGAGAAACTATTTAGACCAAATAATGCGATTTCCCTTGCATGGAATGTTCGCAAAATTACTCG
1 AATGAAAAACTATTTAGACCAAATAATGCGATTTCCCTCACATGGAATGTTCGCAAAATTACTCG
* * *
5833 AGA-GAATGGATCGTCTTGAACCCTTTAATTAA-ATGAAGCTATAAACA-AACTTGTAAAAGTTT
66 A-ACGAATGGATCGTCTTGAACACTTTAATGAACAT-AAGCTATAAA-AGAACTCGTAAAAGTTT
* * **
5895 TTCAATTTCAGAATTTCGTCCAAGAACCAAGAGAGAAACAATTCTCATGTAAATAAGTTTTTAAT
128 GTCAATTTCAGAATTTCGTCCAAGAACAAAGAGAGAAACAATTCTCATGTAAATAAAATTTTAAT
* *
5960 TCGAAGATAAAAACTTGTTTACGA
193 TCAAAGATAAAAACTTGTTTACAA
* *
5984 AATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCACATGGAATGTTCGTAAAATTACTCG
1 AATGAAAAACTATTTAGACCAAATAATGCGATTTCCCTCACATGGAATGTTCGCAAAATTACTCG
*
6049 AACGAATGGATCGTCTTGAGCACTTTAATGAACATAAGCTATAAAAGAACTCGTAAAAGTTTGTC
66 AACGAATGGATCGTCTTGAACACTTTAATGAACATAAGCTATAAAAGAACTCGTAAAAGTTTGTC
* ** *
6114 AATTTTAGAATTTCGTCCAAGAAGTAAGGGAGAAACAATT
131 AATTTCAGAATTTCGTCCAAGAACAAAGAGAGAAACAATT
6154 TCGAAGTTAT
Statistics
Matches: 325, Mismatches: 54, Indels: 14
0.83 0.14 0.04
Matches are distributed among these distances:
215 2 0.01
216 319 0.98
217 4 0.01
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (216 bp):
AATGAAAAACTATTTAGACCAAATAATGCGATTTCCCTCACATGGAATGTTCGCAAAATTACTCG
AACGAATGGATCGTCTTGAACACTTTAATGAACATAAGCTATAAAAGAACTCGTAAAAGTTTGTC
AATTTCAGAATTTCGTCCAAGAACAAAGAGAGAAACAATTCTCATGTAAATAAAATTTTAATTCA
AAGATAAAAACTTGTTTACAA
Found at i:6438 original size:289 final size:288
Alignment explanation
Indices: 5909--6442 Score: 813
Period size: 289 Copynumber: 1.8 Consensus size: 288
5899 ATTTCAGAAT
* *
5909 TTCGTCCAAGAACCAAGAGAGAAACAATTCTCATGTAAATAAGTTTTTAATTCGAAGATAAAAAC
1 TTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATAAAAAC
* * * *
5974 TTGTTTACGAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCACATGGAATGTTCGTA
66 TTGTTTACGAAATGAAAAACTATTTAGACCAAATCATACGATTT-CCTCAAATGGAATGTTCGAA
* * * * *
6039 AAATTACTCGAACGAATGGATCGTCTTGAGCACTTTAATGAACATAAGCTATAAAAGAACTCGTA
130 AAACTACTAGAACGAATGGATCGTCATGAACACTTTAATGAACATAAGCTATAAAAGAAATCGTA
* ** *
6104 AAAGTTTGTCAATTTTAGAATTTCGTCCAAGAAGTAAGGGAGAAACAATTTCGAAGTTATAAAAG
195 AAAGTTTGTCAATTTCAGAATTTCGTCCAAGAACCAAGAGAGAAACAATTTCGAAGTTATAAAAG
6169 AACCAGTAACAGTTCGACAAGTTCGGAAA
260 AACCAGTAACAGTTCGACAAGTTCGGAAA
* *
6198 TTCGTCCAAGAACCAAGAGAGACACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAAC
1 TTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATAAAAAC
*
6263 TTGTTTA-GAAAATGAAAAACTATTTAGACCAAATCATACGATTT-CTCGAGAATGGACTGTTCG
66 TTGTTTACG-AAATGAAAAACTATTTAGACCAAATCATACGATTTCCTC-A-AATGGAATGTTCG
* * *
6326 AAAAACTACTAGAAGGAATGGATCGTCATGAATACTTTAATGAAC-TGAAGTTATAAAAGAAATC
128 AAAAACTACTAGAACGAATGGATCGTCATGAACACTTTAATGAACAT-AAGCTATAAAAGAAATC
6390 GTAAAAGTTTGTCAATTTCAGAATTTCGTCCAAGAACCAAGAGAGAAACAATT
192 GTAAAAGTTTGTCAATTTCAGAATTTCGTCCAAGAACCAAGAGAGAAACAATT
6443 CTCACGTAAA
Statistics
Matches: 220, Mismatches: 21, Indels: 8
0.88 0.08 0.03
Matches are distributed among these distances:
287 3 0.01
288 3 0.01
289 214 0.97
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (288 bp):
TTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATAAAAAC
TTGTTTACGAAATGAAAAACTATTTAGACCAAATCATACGATTTCCTCAAATGGAATGTTCGAAA
AACTACTAGAACGAATGGATCGTCATGAACACTTTAATGAACATAAGCTATAAAAGAAATCGTAA
AAGTTTGTCAATTTCAGAATTTCGTCCAAGAACCAAGAGAGAAACAATTTCGAAGTTATAAAAGA
ACCAGTAACAGTTCGACAAGTTCGGAAA
Found at i:6600 original size:78 final size:78
Alignment explanation
Indices: 6471--6627 Score: 314
Period size: 78 Copynumber: 2.0 Consensus size: 78
6461 TAATTCAAAG
6471 ATAAAATCTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGTGATTTCCCATGCATGGAA
1 ATAAAATCTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGTGATTTCCCATGCATGGAA
6536 TGTTCCGAAAATT
66 TGTTCCGAAAATT
6549 ATAAAATCTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGTGATTTCCCATGCATGGAA
1 ATAAAATCTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGTGATTTCCCATGCATGGAA
6614 TGTTCCGAAAATT
66 TGTTCCGAAAATT
6627 A
1 A
6628 CTCGAAGGAA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (78 bp):
ATAAAATCTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGTGATTTCCCATGCATGGAA
TGTTCCGAAAATT
Found at i:6680 original size:294 final size:293
Alignment explanation
Indices: 6258--6807 Score: 750
Period size: 294 Copynumber: 1.9 Consensus size: 293
6248 TTCAAAGATC
* * *
6258 AAAACTTGTTTAGAAAATGAAAAACTATTTAGACCAAATCATACGATTTCTCGAGAATGGACTGT
1 AAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATCATACGATTTCTCCAGAATGGAATGT
* * * * *
6323 TCGAAAAACTACTAGAAGGAATGGATCGTCATGAATACTTTAATGAACTGAAGTTATAAAAGAAA
66 TCGAAAAACTACTAGAAGGAATGGATCGTCATGAACACTCTAAGGAACCGAAGTTAGAAAAGAAA
* * * * * *
6388 TCGTAAAAGTTTGTCAATTTC-AGAATTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAA
131 TCGTAAAAGTTTGACAAGTTCGA-AAGTTCGTCCAACAACAAAAAGAGAAACAATTCTCACGTAA
*
6452 ATAAGTTTTTAATTC-AAAGATAAAATCTTGTTTACAAAATGAAAAACTATTTAGACCAAATGAT
195 ATAAGTTTTTAATTCGAAAGACAAAA-CTTGTTTACAAAATGAAAAACTATTTAGACCAAATGAT
6516 GTGATTTCCCATGCATGGAATGTTCCGAAAATTAT
259 GTGATTTCCCATGCATGGAATGTTCCGAAAATTAT
* ** *
6551 AAAATCTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGTGATTTC-CCATGCATGGAAT
1 AAAA-CTTGTTTACAAAATGAAAAACTATTTAGACCAAATCATACGATTTCTCCA-GAATGGAAT
* * *
6615 GTTCCG-AAAATTACTCGAAGGAATGGATCGTCTTGAACACTCTAAGGAACCGAA-TATAGAAAA
64 GTT-CGAAAAACTACTAGAAGGAATGGATCGTCATGAACACTCTAAGGAACCGAAGT-TAGAAAA
*
6678 GAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAACAACAAAAAGAGAAACAATTCTCACG
127 GAAATCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAACAACAAAAAGAGAAACAATTCTCACG
* * * ** *
6743 TAAATAAGTTTTTAATTCGAAGGCCAAAACTTGTTTACAAAGTGAAAATTTTTTTAGACCAAATG
192 TAAATAAGTTTTTAATTCGAAAGACAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATG
6808 CTACGACTTC
Statistics
Matches: 222, Mismatches: 29, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
293 7 0.03
294 205 0.92
295 10 0.05
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (293 bp):
AAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATCATACGATTTCTCCAGAATGGAATGT
TCGAAAAACTACTAGAAGGAATGGATCGTCATGAACACTCTAAGGAACCGAAGTTAGAAAAGAAA
TCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAACAACAAAAAGAGAAACAATTCTCACGTAAA
TAAGTTTTTAATTCGAAAGACAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGT
GATTTCCCATGCATGGAATGTTCCGAAAATTAT
Found at i:6930 original size:216 final size:216
Alignment explanation
Indices: 6551--7987 Score: 1609
Period size: 216 Copynumber: 6.7 Consensus size: 216
6541 CGAAAATTAT
* *
6551 AAAATCTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGTGATTTCCCATGCATGGAATG
1 AAAA-CTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCAAGCATGGAATG
* * ** *
6616 TTCCGAAAATTACTCGAAGGAATGGATCGTCTTGAACACTCTAAGGAACCGAATATAGAAAAGAA
65 TTCAGAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGCTATAAAAGAA
* * *
6681 CTCGTAAAAGTTTGACAAGTT-CGAAAGTTCGTCCAACAACAAAAAGAGAAACAATTCTCACGTA
130 CTCGTAAAAGTTCGACAAGTTCCG-AAGTTCGTCCAACAACCAAGAGAGAAACAATTCTCACGTA
* **
6745 AATAAGTTTTTAATTCGAAGGCC
194 AATAAGTTTTTAATTCAAAGATC
* ** * * * * * **
6768 AAAACTTGTTTACAAAGTGAAAATTTTTTTAGACCAAATGCTACGACTTCCCAAGAATATAATGT
1 AAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCAAGCATGGAATGT
* * * ** *
6833 TCAGAAAATTGCTCGAAGGATTGGACCGTCTTGATTACTTTAAGGAACCGAAGCTATAAAATAAC
66 TCAGAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGCTATAAAAGAAC
* * *
6898 TCGTAAAAGTTCGACAAGTTCCGAAGTTCGTCCAAGAACCAAGAGAGACACAATTCTCCCGTAAA
131 TCGTAAAAGTTCGACAAGTTCCGAAGTTCGTCCAACAACCAAGAGAGAAACAATTCTCACGTAAA
*
6963 TAAGTTTTTAATTCACAGATC
196 TAAGTTTTTAATTCAAAGATC
* * * ** * *
6984 AAAACTTGTCTACAAAATGAAAAATTATTTAGACCAAATGATGCGATTTTCTGAGAATGGATTGT
1 AAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCAAGCATGGAATGT
* ** * * * * * *
7049 TC-GAAAACTGTTAGAAGGAATGGATCATCTTGAATACTTTAATGAACTGAAGCTACAAAAGAAC
66 TCAGAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGCTATAAAAGAAC
* * * * * * *
7113 TCGTAAAAGTTTCTA-AATTTCAGAATTTCGTCCAAAAACCAAGAGAGAAACAATTCTCATGGAA
131 TCGTAAAAG-TTCGACAAGTTCCGAAGTTCGTCCAACAACCAAGAGAGAAACAATTCTCACGTAA
7177 ATAAGTTTTTAATTCAAAGATC
195 ATAAGTTTTTAATTCAAAGATC
* * **
7199 AAAACTTGTTTACAAAATAAAAAACTATTTAGACCAAATGATACGATTTCCCTCGCATGGAATGT
1 AAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCAAGCATGGAATGT
* * * * * *
7264 TCGGTAAATTACTCGAAGGAATGGATCATCTTGAACACTTTAATGAACTGAAGCTATAACAGAAC
66 TCAGAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGCTATAAAAGAAC
* * * * ** * * * * * *
7329 TCATAAAAGTTTGTCAATTTTAGAATTTCATCCAAGAGCCAAGAGGGAAACAATTATCACGTAAA
131 TCGTAAAAGTTCGACAAGTTCCGAAGTTCGTCCAACAACCAAGAGAGAAACAATTCTCACGTAAA
7394 TAAGTTTTTAATTCAAAGATC
196 TAAGTTTTTAATTCAAAGATC
*** **
7415 AAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATAATATTTCCCTCGCATGGAATGT
1 AAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCAAGCATGGAATGT
* ** *
7480 TCCA-AAAATCAC-CTGAAGGAATGGATCGTCTTGAACACTTTAAGGAACC-AGATTTAAAAAAG
66 T-CAGAAAATTACTC-GAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGA-AGCTATAAAAG
* * * *
7542 AACTCGTAAGAGTTTGACAAGTTCGGAAGTTCGTACAACAACCAAGAGAGAAACAATTCTCACGT
128 AACTCGTAAAAGTTCGACAAGTTCCGAAGTTCGTCCAACAACCAAGAGAGAAACAATTCTCACGT
* * **
7607 CAACAAGTTTTTAATTCAAAGGCC
193 AAATAAGTTTTTAATTCAAAGATC
** * *
7631 AAAA-TATGTTTACAAAATGACGAAC-ATTTTAGACCAAATGATGCGAGTTCCCAAGCATGTAAT
1 AAAACT-TGTTTACAAAATGAAAAACTA-TTTAGACCAAATGATGCGATTTCCCAAGCATGGAAT
* * * * *
7694 GTTC-GAAAAATTGCTTGAAGGATTGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAG
64 GTTCAG-AAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGCTATAAAAG
* * * * * *
7758 AAATAGTAACAGTTCGACAAGTT-CGAAAGTTCGTCCAATAACCAAGAGAGACACAATTTTCACG
128 AACTCGTAAAAGTTCGACAAGTTCCG-AAGTTCGTCCAACAACCAAGAGAGAAACAATTCTCACG
* *
7822 TAAATAAGCTTTTAATTCAAATATC
192 TAAATAAGTTTTTAATTCAAAGATC
* *
7847 AAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCAG-ATGAAATG
1 AAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCC-AAGCATGGAATG
* * * * ** *
7911 TTCACAAAATTACTCGAAGGAACGGATCGTCTTGAACACTTGAATGAACATAAGCTATGAAAGAA
65 TTCAGAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGCTATAAAAGAA
7976 CTCGTAAAAGTT
130 CTCGTAAAAGTT
7988 TGTCAATTTT
Statistics
Matches: 1024, Mismatches: 178, Indels: 37
0.83 0.14 0.03
Matches are distributed among these distances:
215 187 0.18
216 825 0.81
217 12 0.01
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.27
Consensus pattern (216 bp):
AAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCAAGCATGGAATGT
TCAGAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGCTATAAAAGAAC
TCGTAAAAGTTCGACAAGTTCCGAAGTTCGTCCAACAACCAAGAGAGAAACAATTCTCACGTAAA
TAAGTTTTTAATTCAAAGATC
Found at i:8263 original size:287 final size:286
Alignment explanation
Indices: 7744--8314 Score: 851
Period size: 287 Copynumber: 2.0 Consensus size: 286
7734 TTTAAGGAAC
*
7744 CGAAGTTATAAAAGAAATAGTAACAGTTCGACAAGTTCGAAAGTTCGTCCAATAACCAAGAGAGA
1 CGAAGTTATAAAAGAAATAGTAACAGTTCGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGA
* *
7809 CACAATTTTCACGTAAATAAGCTTTTAATTCAAATATCAAAACTTGTTTACAAAATGAAAAACTA
66 CACAATTCTCACGTAAATAAGCTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAAAAACTA
* * *
7874 TTTAGACCAAATGATGCGATTTCCCTCAGATGAAATGTTCACAAAATTACTCGAAGGAACGGATC
131 TTTAGACCAAATGATACGATTT-CCTCAGATGAAATGTTCACAAAACTACTAGAAGGAACGGATC
* * *
7939 GTCTTGAACACTTGAATGAACATAAGCTATGAAAGAACTCGTAAAAGTTTGTCAATTTTAGAATT
195 GTCTTGAACACTTGAATGAACATAAGCTATAAAAGAACCCGTAAAAGTTTGTCAATTTCAGAATT
* *
8004 TCGTCCAGGAACCAAGGGAGAAACGAT
260 TCGTCCAAGAACCAAGAGAGAAACGAT
*
8031 CGAAGTTATAAAAGAACTAGTAACAGTTCGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGA
1 CGAAGTTATAAAAGAAATAGTAACAGTTCGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGA
* *
8096 CACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTAGAAAATGAAAAACTA
66 CACAATTCTCACGTAAATAAGCTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAAAAACTA
* * * * *
8161 TTTAGACCAAATGATACGATTT-CTCGAGAATGGATTGTTCGA-AAAGCTGCTAGAAGGAATGGA
131 TTTAGACCAAATGATACGATTTCCTC-AG-ATGAAATGTTC-ACAAAACTACTAGAAGGAACGGA
* * * * *
8224 TTGTCTTGAATACTTTAATGAAC-TGATGTTATAAAAGAACCCGTAAAAGTTTGTCAATTTCAGA
193 TCGTCTTGAACACTTGAATGAACAT-AAGCTATAAAAGAACCCGTAAAAGTTTGTCAATTTCAGA
*
8288 ATTTCGTCTAAGAACCAAGAGAGAAAC
257 ATTTCGTCCAAGAACCAAGAGAGAAAC
8315 AATTCTCATG
Statistics
Matches: 255, Mismatches: 25, Indels: 8
0.89 0.09 0.03
Matches are distributed among these distances:
285 3 0.01
286 3 0.01
287 248 0.97
288 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (286 bp):
CGAAGTTATAAAAGAAATAGTAACAGTTCGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGA
CACAATTCTCACGTAAATAAGCTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAAAAACTA
TTTAGACCAAATGATACGATTTCCTCAGATGAAATGTTCACAAAACTACTAGAAGGAACGGATCG
TCTTGAACACTTGAATGAACATAAGCTATAAAAGAACCCGTAAAAGTTTGTCAATTTCAGAATTT
CGTCCAAGAACCAAGAGAGAAACGAT
Found at i:8435 original size:216 final size:215
Alignment explanation
Indices: 8040--8623 Score: 669
Period size: 216 Copynumber: 2.7 Consensus size: 215
8030 TCGAAGTTAT
** * * * *
8040 AAAAGAACTAGTAACAGTTCGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGACACAATTCT
1 AAAAGAACCCGTAAAAGTTTGACAAGTTAGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCT
*
8105 CACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTA-GAAAATGAAAAACTATTTAGACC
66 CATGTAAATAAGTTTTTAATTCAAAGAT-AAAACTTGTTTACG-AAATGAAAAACTATTTAGACC
* * * * * *
8169 AAATGATACGATTTCTCGAGAATGGATTGTTCGAAAAGCTGCTAGAAGGAATGGATTGTCTTGAA
129 AAATGATGCGATTTCCCGAGAATGGAATGTTCGAAAAGCTACCAGAAGGAATGGATCGTCTTGAA
* * * * * * *
8234 TACTTTAATGAA-CTGATGTTAT
194 CAATCTAAGGAACCAGAT-ATAG
* * * *
8256 AAAAGAACCCGTAAAAGTTTGTCAATTTCAG-AATTTCGTCTAAGAACCAAGAGAGAAACAATTC
1 AAAAGAACCCGTAAAAGTTTGACAAGTT-AGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTC
* *
8320 TCATGTAAATATGTTTTTAATTCGAAGATAATAACTTGTTTACGAAATGAAAAACTATTTAGACC
65 TCATGTAAATAAGTTTTTAATTCAAAGATAA-AACTTGTTTACGAAATGAAAAACTATTTAGACC
** * * *
8385 AAATGATGCGATTTCCCTTGCATGGAATGTTTCGAAAA-TTACCCGAAGGAATGGATCGTCTTGA
129 AAATGATGCGATTTCCCGAGAATGGAATG-TTCGAAAAGCTACCAGAAGGAATGGATCGTCTTGA
8449 ACAATCTAAGGAACCAGATATAG
193 ACAATCTAAGGAACCAGATATAG
* * *
8472 AAAAGAACTCGTAAAATTTTGACAAGTTAGAAAGTTCGTCCAACAA-CAGAGAGAGAAACAATTC
1 AAAAGAACCCGTAAAAGTTTGACAAGTTAGAAAGTTCGTCCAAGAACCA-AGAGAGAAACAATTC
* ** *
8536 TC-TCATAAATAAGTTTTTAATTCAAAGGCCAAAACTTGTTTAC-AAAGTGAAAAACTTTTTAGA
65 TCAT-GTAAATAAGTTTTTAATTCAAA-GATAAAACTTGTTTACGAAA-TGAAAAACTATTTAGA
* *
8599 CCAAATGATGCGACTTCCCAAGAAT
127 CCAAATGATGCGATTTCCCGAGAAT
8624 ATAAT
Statistics
Matches: 310, Mismatches: 48, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
215 10 0.03
216 283 0.91
217 17 0.05
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (215 bp):
AAAAGAACCCGTAAAAGTTTGACAAGTTAGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCT
CATGTAAATAAGTTTTTAATTCAAAGATAAAACTTGTTTACGAAATGAAAAACTATTTAGACCAA
ATGATGCGATTTCCCGAGAATGGAATGTTCGAAAAGCTACCAGAAGGAATGGATCGTCTTGAACA
ATCTAAGGAACCAGATATAG
Found at i:8484 original size:503 final size:502
Alignment explanation
Indices: 7537--8492 Score: 1253
Period size: 503 Copynumber: 1.9 Consensus size: 502
7527 CCAGATTTAA
* * * *
7537 AAAAGAACTCGTAAGAGTTTGACAAGTTCGGAAGTTCGTACAACAACCAAGAGAGAAACAATTCT
1 AAAAGAACTAGTAACAGTTCGACAAGTTCGAAAGTTCGTACAACAACCAAGAGAGAAACAATTCT
* * **
7602 CACGTCAACAAGTTTTTAATTCAAAGGCCAAAATATGTTTACAAAATGACGAACATTTTAGACCA
66 CACGTAAACAAGTTTTTAATTCAAAGACCAAAATATGTTTACAAAATGAAAAACATTTTAGACCA
* * * * * *
7667 AATGATGCGAGTTCCCAAGCATGTAATGTTCGAAAAATTGCTTGAAGGATTGGATCGTCTTGAAT
131 AATGATACGAGTTCCCAAGAATGGAATGTTCGAAAAACTGCTAGAAGGAATGGATCGTCTTGAAT
* * *
7732 ACTTTAAGGAACCGAAGTTATAAAAGAAATAGTAACAGTTCGACAAGTTCGAAAGTTCGTCCAAT
196 ACTTTAAGGAACCGAAGTTATAAAAGAAACAGTAAAAGTTCGACAAGTTCGAAAGTTCGTCCAAG
* * *
7797 AACCAAGAGAGACACAATTTTCACGTAAATAAGCTTTTAATTCAAATATCAAAACTTGTTTACAA
261 AACCAAGAGAGAAACAATTCTCACGTAAATAAGCTTTTAATTCAAAGATCAAAACTTGTTTACAA
*
7862 AATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCAGATGAAATGTTCACAAAATTACTCG
326 AATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCAGATGAAATGTTCACAAAATTACCCG
* * *
7927 AAGGAACGGATCGTCTTGAACACTTGAATGAACATAAGCTATGAAAGAACTCGTAAAAGTTTGTC
391 AAGGAACGGATCGTCTTGAACAATTGAAGGAACA-AAGATATGAAAGAACTCGTAAAAGTTTGTC
7992 AATTTTAGAATTTCGTCCAGGAACCAAGGGAGAAACGATCGAAGTTAT
455 AATTTTAGAATTTCGTCCAGGAACCAAGGGAGAAACGATCGAAGTTAT
* * *
8040 AAAAGAACTAGTAACAGTTCGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGACACAATTCT
1 AAAAGAACTAGTAACAGTTCGACAAGTTCGAAAGTTCGTACAACAACCAAGAGAGAAACAATTCT
* * *
8105 CACGTAAATAAGTTTTTAATTCAAAGATCAAAACT-TGTTTAGAAAATGAAAAAC-TATTTAGAC
66 CACGTAAACAAGTTTTTAATTCAAAGACCAAAA-TATGTTTACAAAATGAAAAACAT-TTTAGAC
* * * * * *
8168 CAAATGATACGATTTCTCGAGAATGGATTGTTCGAAAAGCTGCTAGAAGGAATGGATTGTCTTGA
129 CAAATGATACGAGTTCCCAAGAATGGAATGTTCGAAAAACTGCTAGAAGGAATGGATCGTCTTGA
* * * * * * * * * *
8233 ATACTTTAATGAACTGATGTTATAAAAGAACCCGTAAAAGTTTGTCAATTTC-AGAATTTCGTCT
194 ATACTTTAAGGAACCGAAGTTATAAAAGAAACAGTAAAAGTTCGACAAGTTCGA-AAGTTCGTCC
* * * *
8297 AAGAACCAAGAGAGAAACAATTCTCATGTAAATATGTTTTTAATTCGAAGAT-AATAACTTGTTT
258 AAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGCTTTTAATTCAAAGATCAA-AACTTGTTT
* * * *
8361 ACGAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCT-TGCATGGAATGTTTC-GAAAAT
322 ACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCAG-ATGAAATG-TTCACAAAAT
* *
8424 TACCCGAAGGAATGGATCGTCTTGAACAATCT-AAGGAAC-CAGATATAGAAAAGAACTCGTAAA
385 TACCCGAAGGAACGGATCGTCTTGAACAAT-TGAAGGAACAAAGATAT-G-AAAGAACTCGTAAA
*
8487 ATTTTG
447 AGTTTG
8493 ACAAGTTAGA
Statistics
Matches: 387, Mismatches: 57, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
501 5 0.01
502 6 0.02
503 371 0.96
504 5 0.01
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (502 bp):
AAAAGAACTAGTAACAGTTCGACAAGTTCGAAAGTTCGTACAACAACCAAGAGAGAAACAATTCT
CACGTAAACAAGTTTTTAATTCAAAGACCAAAATATGTTTACAAAATGAAAAACATTTTAGACCA
AATGATACGAGTTCCCAAGAATGGAATGTTCGAAAAACTGCTAGAAGGAATGGATCGTCTTGAAT
ACTTTAAGGAACCGAAGTTATAAAAGAAACAGTAAAAGTTCGACAAGTTCGAAAGTTCGTCCAAG
AACCAAGAGAGAAACAATTCTCACGTAAATAAGCTTTTAATTCAAAGATCAAAACTTGTTTACAA
AATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCAGATGAAATGTTCACAAAATTACCCG
AAGGAACGGATCGTCTTGAACAATTGAAGGAACAAAGATATGAAAGAACTCGTAAAAGTTTGTCA
ATTTTAGAATTTCGTCCAGGAACCAAGGGAGAAACGATCGAAGTTAT
Done.