Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold577
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: 68063
ACGTcount: A:0.13, C:0.06, G:0.07, T:0.13
Warning! 40823 characters in sequence are not A, C, G, or T
Found at i:1405 original size:33 final size:33
Alignment explanation
Indices: 1368--1436 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
1358 TTTTTATTCA
*
1368 TAATAAATATGCTTTTCTTTTATTTAATAATGG
1 TAATAAATATGCTTTTCATTTATTTAATAATGG
1401 TAATAAATATGCTTTTCATTTATTTAATAATGG
1 TAATAAATATGCTTTTCATTTATTTAATAATGG
1434 TAA
1 TAA
1437 AATCGTAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.49
Consensus pattern (33 bp):
TAATAAATATGCTTTTCATTTATTTAATAATGG
Found at i:1740 original size:23 final size:25
Alignment explanation
Indices: 1714--1764 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
1704 TTTTCACCAC
*
1714 AAAATCAT-AAA-ATTATTTAATTT
1 AAAATCATAAAATATTATTGAATTT
**
1737 AAAATTTTAAAATATTATTGAATTT
1 AAAATCATAAAATATTATTGAATTT
1762 AAA
1 AAA
1765 TTTTAGATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 6 0.26
24 3 0.13
25 14 0.61
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (25 bp):
AAAATCATAAAATATTATTGAATTT
Found at i:1896 original size:22 final size:24
Alignment explanation
Indices: 1869--1932 Score: 82
Period size: 22 Copynumber: 2.8 Consensus size: 24
1859 TTATTTAAAA
1869 TAAATAAATTAATATTATTAAA-G
1 TAAATAAATTAATATTATTAAATG
1892 -AAATAAATTAA-ATTACTTAAATG
1 TAAATAAATTAATATTA-TTAAATG
*
1915 TTAATAAA-TAATATTATT
1 TAAATAAATTAATATTATT
1933 GAAAATGTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
21 4 0.11
22 16 0.44
23 6 0.17
24 10 0.28
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.41
Consensus pattern (24 bp):
TAAATAAATTAATATTATTAAATG
Found at i:16252 original size:3 final size:3
Alignment explanation
Indices: 16246--16276 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
16236 TTTATCTTAC
*
16246 TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
16277 ATACATACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:21237 original size:13 final size:13
Alignment explanation
Indices: 21199--21229 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
21189 GTGATGTGAA
21199 AAAATGAAAAGATG
1 AAAATGAAAA-ATG
21213 AAAATGAAAAATG
1 AAAATGAAAAATG
21226 AAAA
1 AAAA
21230 GTAAAAATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (13 bp):
AAAATGAAAAATG
Found at i:21585 original size:35 final size:35
Alignment explanation
Indices: 21539--21610 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
21529 GGGCACCTAA
21539 TCTTGGAACACTTCATTCATTGCCAAGATACGCAT
1 TCTTGGAACACTTCATTCATTGCCAAGATACGCAT
21574 TCTTGGAACACTTCATTCATTGCCAAGATACGCAT
1 TCTTGGAACACTTCATTCATTGCCAAGATACGCAT
21609 TC
1 TC
21611 CTAAATCAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (35 bp):
TCTTGGAACACTTCATTCATTGCCAAGATACGCAT
Found at i:22718 original size:133 final size:131
Alignment explanation
Indices: 22542--23178 Score: 799
Period size: 133 Copynumber: 4.8 Consensus size: 131
22532 TTGAAAATAT
* * * * *
22542 CAGATATTGCCTTCCTACATATACAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTAAGG
1 CAGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCGAAGATGGCGGATTTTACCTCCCT--GG
* * *
22607 TTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGTAGCAGCGGAATAGATTGAAGA
64 TTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTAAAGA
**
22672 TTT
129 TAG
* * * * *
22675 TAGATCTTGCCTTCCTGCATAGACAACAAAGAAGATCGAAGATGGCAGATTTTACCTCCTCGTGG
1 CAGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCGAAGATGGCGGATTTTACCTCC-C-TGG
* *
22740 TTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGTAATAGATTGAAGA
64 TTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTAAAGA
22805 TAG
129 TAG
* * * *
22808 CAGATCTTGCTTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCGAATTTTACCTCTTCGTGG
1 CAGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCGAAGATGGCGGATTTTACCTC--CCTGG
*
22873 TTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCATCGGAATAGATTAAAGA
64 TTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTAAAGA
**
22938 TTT
129 TAG
* * * **
22941 TAGATCTTGCCTTCCTGCATAGACAGCGAAGAAGATCGAAGACGGTAGATTTTACCTCCCTGTGG
1 CAGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCGAAGATGGCGGATTTTACCTCCC--TGG
* * * *
23006 TTACAGTGAAGTACATTGAAGCC-GATAATTTTACTTCTCTGGGCAGCAGTGGAATAGATTAAAG
64 TTACAGTGGAGTACATTGAAGCCAG-TAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTAAAG
23070 ATAG
128 ATAG
** * * * * *
23074 CAGATCTTGTATTCCTACATAGACAGCGAAGTAGATCAAAAATGGAGGATTTTACCTCATCGTGG
1 CAGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCGAAGATGGCGGATTTTACCTC--CCTGG
*
23139 TTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT
64 TTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT
23179 AGCAGATCTT
Statistics
Matches: 434, Mismatches: 60, Indels: 20
0.84 0.12 0.04
Matches are distributed among these distances:
131 1 0.00
132 1 0.00
133 427 0.98
134 2 0.00
135 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.28
Consensus pattern (131 bp):
CAGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCGAAGATGGCGGATTTTACCTCCCTGGTT
ACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTAAAGATA
G
Found at i:23027 original size:266 final size:265
Alignment explanation
Indices: 22532--23178 Score: 951
Period size: 266 Copynumber: 2.4 Consensus size: 265
22522 AGAGAGCAGG
* * * * * * *
22532 TTGAAAATATCAGATATTGCCTTCCTACATATACAGTGGAGCAGATCGAAGATGGCGGATTTTAC
1 TTGAAGATAGCAGATCTTGCTTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCGGATTTTAC
* * *
22597 CTC-CCTAAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGTAGCAGCGGAA
66 CTCTCGT--GGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAA
* *
22661 TAGATTGAAGATTTTAGATCTTGCCTTCCTGCATAGACAACAAAGAAGATCGAAGATGGCAGATT
129 TAGATTAAAGATTTTAGATCTTGCCTTCCTGCATAGACAACAAAGAAGATCGAAGACGGCAGATT
*
22726 TTACCTCCTCGTGGTTACAGTGGAGTACATTGAAGCC-AGTAATTCTACTTCCCTGGGCAGCAGC
194 TTACCTCCTCGTGGTTACAGTGAAGTACATTGAAGCCGA-TAATTCTACTTCCCTGGGCAGCAGC
*
22790 GTAATAGA
258 GGAATAGA
*
22798 TTGAAGATAGCAGATCTTGCTTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCGAATTTTAC
1 TTGAAGATAGCAGATCTTGCTTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCGGATTTTAC
*
22863 CTCTTCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCATCGGAAT
66 CTC-TCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAAT
* * *
22928 AGATTAAAGATTTTAGATCTTGCCTTCCTGCATAGACAGCGAAGAAGATCGAAGACGGTAGATTT
130 AGATTAAAGATTTTAGATCTTGCCTTCCTGCATAGACAACAAAGAAGATCGAAGACGGCAGATTT
* * *
22993 TACCTCC-CTGTGGTTACAGTGAAGTACATTGAAGCCGATAATTTTACTTCTCTGGGCAGCAGTG
195 TACCTCCTC-GTGGTTACAGTGAAGTACATTGAAGCCGATAATTCTACTTCCCTGGGCAGCAGCG
23057 GAATAGA
259 GAATAGA
* * * * *
23064 TTAAAGATAGCAGATCTTG-TATTCCTACATAGACAGCGAAGTAGATCAAAAATGGAGGATTTTA
1 TTGAAGATAGCAGATCTTGCT-TTCCTACATAGACAGCGAAGCAGATCGAAGATGGCGGATTTTA
*
23128 CCTCATCGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT
65 CCTC-TCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT
23179 AGCAGATCTT
Statistics
Matches: 346, Mismatches: 30, Indels: 10
0.90 0.08 0.03
Matches are distributed among these distances:
265 2 0.01
266 341 0.99
267 1 0.00
268 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (265 bp):
TTGAAGATAGCAGATCTTGCTTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCGGATTTTAC
CTCTCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATA
GATTAAAGATTTTAGATCTTGCCTTCCTGCATAGACAACAAAGAAGATCGAAGACGGCAGATTTT
ACCTCCTCGTGGTTACAGTGAAGTACATTGAAGCCGATAATTCTACTTCCCTGGGCAGCAGCGGA
ATAGA
Found at i:23257 original size:107 final size:107
Alignment explanation
Indices: 23071--23285 Score: 351
Period size: 107 Copynumber: 2.0 Consensus size: 107
23061 AGATTAAAGA
* *
23071 TAGCAGATCTTGTATTCCTACATAGACAGCGAAGTAGATCAAAAATGGAGGATTTTACCTCATCG
1 TAGCAGATCTTGCATTCCTACATAGACAGCGAAGCAGATCAAAAATGGAGGATTTTACCTCATCG
*
23136 TGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
66 TGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
* * * *
23178 TAGCAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCA-GATTTTACCTCCTC
1 TAGCAGATCTTGCATTCCTACATAGACAGCGAAGCAGATCAAAAATGG-AGGATTTTACCTCATC
23242 GTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
65 GTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
23285 T
1 T
23286 GGGTAGCAGC
Statistics
Matches: 100, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
107 99 0.99
108 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (107 bp):
TAGCAGATCTTGCATTCCTACATAGACAGCGAAGCAGATCAAAAATGGAGGATTTTACCTCATCG
TGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
Found at i:23367 original size:240 final size:240
Alignment explanation
Indices: 22942--23420 Score: 680
Period size: 240 Copynumber: 2.0 Consensus size: 240
22932 TAAAGATTTT
* *
22942 AGATCTTGCCTTCCTGCATAGACAGCGAAGAAGATCGAAGACGGTAGATTTTACCTCCCTGTGGT
1 AGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCGAAGACGGCAGATTTTACCTCCCTGTGGT
* * *
23007 TACAGTGAAGTACATTGAAGCCGATAATTTTACTTCTCTGGGCAGCAGTGGAATAGATTAAAGAT
66 TACAGTGAAGTACATTGAAGCCGATAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTAAAGAT
* * * *
23072 AGCAGATCTTGTATTCCTACATAGACAGCGAAGTAGATCAAAAATGGAGGATTTTACCT-CATCG
131 AGCAGATCTTGCATTCCTACATAGACAGCGAAGAAGATCAAAAACGGAGGATTTTACCTCCCT-G
*
23136 TGGTTATAGTGGAGTACATTGAAGCC-AGTAATTCTACTTCCCTAGC
195 TGGTTACAGTGGAGTACATTGAAGCCGA-TAATTCTACTTCCCTAGC
* *
23182 AGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCAGATTTTACCT-CCTCGTGG
1 AGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCGAAGACGGCAGATTTTACCTCCCT-GTGG
* * *
23246 TTACAGTGGAGTACATTGAAGCC-AGTAATTCTACTTCCCTGGGTAGCAGCGGAATAGATTGAAG
65 TTACAGTGAAGTACATTGAAGCCGA-TAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTAAAG
*** * * * *
23310 ATTTTAGATCTTGCCTTCCTGCATAGACAGCGAAGAAGATCGAAGACGGTA-GATTTTACCTCCC
129 ATAGCAGATCTTGCATTCCTACATAGACAGCGAAGAAGATCAAAAACGG-AGGATTTTACCTCCC
23374 TGTGGTTACAGTGGAGTACATTGAAGCCGATAATTCTACTTCCCTAG
193 TGTGGTTACAGTGGAGTACATTGAAGCCGATAATTCTACTTCCCTAG
23421 GCAGCAGTGG
Statistics
Matches: 212, Mismatches: 22, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
239 4 0.02
240 204 0.96
241 4 0.02
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (240 bp):
AGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCGAAGACGGCAGATTTTACCTCCCTGTGGT
TACAGTGAAGTACATTGAAGCCGATAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTAAAGAT
AGCAGATCTTGCATTCCTACATAGACAGCGAAGAAGATCAAAAACGGAGGATTTTACCTCCCTGT
GGTTACAGTGGAGTACATTGAAGCCGATAATTCTACTTCCCTAGC
Found at i:23427 original size:133 final size:133
Alignment explanation
Indices: 23180--23936 Score: 972
Period size: 133 Copynumber: 5.7 Consensus size: 133
23170 TACTTCCCTA
*
23180 GCAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCTCGTG
1 GCAGATCTTGCCTTCCTACATAGACAGTGAAGCAGATCGAAGATGGCAGATTTTACCTCCTCGTG
* *
23245 GTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGTAGCAGCGGAATAGATTGAAG
66 GTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAG
23310 ATT
131 ATT
** * * * * *
23313 TTAGATCTTGCCTTCCTGCATAGACAGCGAAGAAGATCGAAGACGGTAGATTTTACCTCC-CTGT
1 GCAGATCTTGCCTTCCTACATAGACAGTGAAGCAGATCGAAGATGGCAGATTTTACCTCCTC-GT
* *
23377 GGTTACAGTGGAGTACATTGAAGCC-GATAATTCTACTTCCCTAGGCAGCAGTGGAATAGATTAA
65 GGTTACAGTGGAGTACATTGAAGCCAG-TAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGA
*
23441 AGATA
129 AGATT
* * * *
23446 GCAGATCTTGCCTTCCTACATAGACAGTGAAGTAGATCAAAAATGGCAGATTTTACCTCATCGTG
1 GCAGATCTTGCCTTCCTACATAGACAGTGAAGCAGATCGAAGATGGCAGATTTTACCTCCTCGTG
* * *
23511 GTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCTTGGGCAGCAGCGGAATAGATTGACG
66 GTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAG
*
23576 ATA
131 ATT
*
23579 GCAGATCTTGCCTTCCTACATAGACAGTGAAGCAGATCGAAGATGGCGGATTTTACCTCCTCGTG
1 GCAGATCTTGCCTTCCTACATAGACAGTGAAGCAGATCGAAGATGGCAGATTTTACCTCCTCGTG
*
23644 GTTACAGTGGAGTACATTGAAGCCAGTAATTCTA-TCTCCCTGGGCAGCAGTGGAATAGACTGAA
66 GTTACAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCCTGGGCAGCAGTGGAATAGATTGAA
23708 GATT
130 GATT
* * * * * * * * * * * *
23712 TCATATATTGTCTCCCTAAACAG-TAGTGGAGCAGATCAAAGATGGCAGAATTTACTTCC-CTGT
1 GCAGATCTTGCCTTCCTACATAGACAGTGAAGCAGATCGAAGATGGCAGATTTTACCTCCTC-GT
*
23775 GGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTAGGGCAACAGTGGAATAGATTGA
65 GGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT-GGGCAGCAGTGGAATAGATTGA
23840 AGATT
129 AGATT
* ** * * * * * * *
23845 ACAGATCTTATCTCCCTA-AGCAG-TAGTGGAGTAGATCGAAGATGGCCGATTCTACCTCC-CTG
1 GCAGATCTTGCCTTCCTACA-TAGACAGTGAAGCAGATCGAAGATGGCAGATTTTACCTCCTC-G
*
23907 AGGTTACAGTGGAGTACATTGAAGCCAGTA
64 TGGTTACAGTGGAGTACATTGAAGCCAGTA
23937 TTCCTATCTC
Statistics
Matches: 553, Mismatches: 62, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
131 1 0.00
132 76 0.14
133 474 0.86
134 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (133 bp):
GCAGATCTTGCCTTCCTACATAGACAGTGAAGCAGATCGAAGATGGCAGATTTTACCTCCTCGTG
GTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAG
ATT
Found at i:23490 original size:373 final size:376
Alignment explanation
Indices: 22804--23936 Score: 1471
Period size: 373 Copynumber: 3.0 Consensus size: 376
22794 TAGATTGAAG
* *
22804 ATAGCAGATCTTGCTTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCGAATTTTACCTCTTC
1 ATAGCAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCG-ATTTTACCTCCTC
* *
22869 GTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCATCGGAATAGATTA
65 GTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTG
22934 AAGATTTTAGATCTTGCCTTCCTGCATAGACAGCGAAGAAGATCGAAGACGGTAGATTTTACCTC
130 AAGATTTTAGATCTTGCCTTCCTGCATAGACAGCGAAGAAGATCGAAGACGGTAGATTTTACCTC
* * * *
22999 CCTGTGGTTACAGTGAAGTACATTGAAGCCGATAATTTTACTTCTCTGGGCAGCAGTGGAATAGA
195 CCTGTGGTTACAGTGGAGTACATTGAAGCCGATAATTCTACTTCCCTAGGCAGCAGTGGAATAGA
* *
23064 TTAAAGATAGCAGATCTTGTATTCCTACATAGACAGCGAAGTAGATCAAAAATGGAGGATTTTAC
260 TTAAAGATAGCAGATCTTGTCTTCCTACATAGACAGTGAAGTAGATCAAAAATGGA-GATTTTAC
*
23129 CTCATCGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTA-CTT-C-C-C
324 CTCATCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACCTTGCACAC
23178 -TAGCAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCTC
1 ATAGCAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGC-GATTTTACCTCCTC
*
23242 GTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGTAGCAGCGGAATAGATTG
65 GTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTG
23307 AAGATTTTAGATCTTGCCTTCCTGCATAGACAGCGAAGAAGATCGAAGACGGTAGATTTTACCTC
130 AAGATTTTAGATCTTGCCTTCCTGCATAGACAGCGAAGAAGATCGAAGACGGTAGATTTTACCTC
23372 CCTGTGGTTACAGTGGAGTACATTGAAGCCGATAATTCTACTTCCCTAGGCAGCAGTGGAATAGA
195 CCTGTGGTTACAGTGGAGTACATTGAAGCCGATAATTCTACTTCCCTAGGCAGCAGTGGAATAGA
*
23437 TTAAAGATAGCAGATCTTGCCTTCCTACATAGACAGTGAAGTAGATCAAAAATGGCAGATTTTAC
260 TTAAAGATAGCAGATCTTGTCTTCCTACATAGACAGTGAAGTAGATCAAAAATGG-AGATTTTAC
23502 CTCATCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCTTGGGCAGCAGCGGAAT
324 CTCATCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA---CCTT-----GCA-C-----
23567 AGATTGAC
375 ------AC
*
23575 GATAGCAGATCTTGCCTTCCTACATAGACAGTGAAGCAGATCGAAGATGGCGGATTTTACCTCCT
1 -ATAGCAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGC-GATTTTACCTCCT
* *
23640 CGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA-TCTCCCTGGGCAGCAGTGGAATAGAC
64 CGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCCTGGGCAGCAGCGGAATAGAT
* * * * * ** * * * * * * * * * *
23704 TGAAGATTTCATATATTGTCTCCCTAAACAG-TAGTGGAGCAGATCAAAGATGGCAGAATTTACT
128 TGAAGATTTTAGATCTTGCCTTCCTGCATAGACAGCGAAGAAGATCGAAGACGGTAGATTTTACC
*
23768 TCCCTGTGGTTACAGTGGAGTACATTGAAGCC-AGTAATTCTACTTCCCTAGGGCAACAGTGGAA
193 TCCCTGTGGTTACAGTGGAGTACATTGAAGCCGA-TAATTCTACTTCCCTA-GGCAGCAGTGGAA
* * * * * * * * *
23832 TAGATTGAAGATTA-CAGATCTTATCTCCCTA-AGCAG-TAGTGGAGTAGATCGAAGATGGCCGA
256 TAGATTAAAGA-TAGCAGATCTTGTCTTCCTACA-TAGACAGTGAAGTAGATCAAAAATGG-AGA
* * *
23894 TTCTACCTC-CCTGAGGTTACAGTGGAGTACATTGAAGCCAGTA
318 TTTTACCTCATC-GTGGTTACAGTGGAGTACATTGAAGCCAGTA
23937 TTCCTATCTC
Statistics
Matches: 676, Mismatches: 49, Indels: 44
0.88 0.06 0.06
Matches are distributed among these distances:
373 350 0.52
374 2 0.00
377 3 0.00
383 1 0.00
385 1 0.00
397 3 0.00
398 133 0.20
399 181 0.27
400 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (376 bp):
ATAGCAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCGATTTTACCTCCTCG
TGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGA
AGATTTTAGATCTTGCCTTCCTGCATAGACAGCGAAGAAGATCGAAGACGGTAGATTTTACCTCC
CTGTGGTTACAGTGGAGTACATTGAAGCCGATAATTCTACTTCCCTAGGCAGCAGTGGAATAGAT
TAAAGATAGCAGATCTTGTCTTCCTACATAGACAGTGAAGTAGATCAAAAATGGAGATTTTACCT
CATCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACCTTGCACAC
Found at i:23632 original size:506 final size:506
Alignment explanation
Indices: 22676--23677 Score: 1523
Period size: 506 Copynumber: 2.0 Consensus size: 506
22666 TGAAGATTTT
*
22676 AGATCTTGCCTTCCTGCATAGACAACAAAGAAGATCGAAGATGGCAGATTTTACCTCCTCGTGGT
1 AGATCTTGCCTTCCTACATAGACAACAAAGAAGATCGAAGATGGCAGATTTTACCTCCTCGTGGT
*
22741 TACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGTAATAGATTGAAGAT
66 TACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAGAT
* * * * *
22806 AGCAGATCTTGCTTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCGAATTTTACCTCTTCGT
131 AGCAGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCGAAGACGGAGAATTTTACCTCCTCGT
*
22871 GGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCATCGGAATAGATTAAA
196 GGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTAGGCAGCATCGGAATAGATTAAA
*** * * * *
22936 GATTTTAGATCTTGCCTTCCTGCATAGACAGCGAAGAAGATCGAAGACGGTAGATTTTACCTCCC
261 GATAGCAGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCAAAAACGGCAGATTTTACCTCCC
* *
23001 TGTGGTTACAGTGAAGTACATTGAAGCCGATAATTTTACTTCTCTGGGCAGCAGTGGAATAGATT
326 TGTGGTTACAGTGAAGTACATTGAAGCCGATAATTCTACTTCTCTGGGCAGCAGCGGAATAGATT
* *
23066 AAAGATAGCAGATCTTGTATTCCTACATAGACAGCGAAGTAGATCAAAAATGGAGGATTTTACCT
391 AAAGATAGCAGATCTTGCATTCCTACATAGACAGCGAAGCAGATCAAAAATGGAGGATTTTACCT
*
23131 CATCGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTAGC
456 CATCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTAGC
* * *
23182 AGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCTCGTGGT
1 AGATCTTGCCTTCCTACATAGACAACAAAGAAGATCGAAGATGGCAGATTTTACCTCCTCGTGGT
*
23247 TACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGTAGCAGCGGAATAGATTGAAGAT
66 TACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAGAT
*** *
23312 TTTAGATCTTGCCTTCCTGCATAGACAGCGAAGAAGATCGAAGACGGTAG-ATTTTACCTCC-CT
131 AGCAGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCGAAGACGG-AGAATTTTACCTCCTC-
23375 GTGGTTACAGTGGAGTACATTGAAGCC-GATAATTCTACTTCCCTAGGCAGCAGT-GGAATAGAT
194 GTGGTTACAGTGGAGTACATTGAAGCCAG-TAATTCTACTTCCCTAGGCAGCA-TCGGAATAGAT
* * *
23438 TAAAGATAGCAGATCTTGCCTTCCTACATAGACAGTGAAGTAGATCAAAAATGGCAGATTTTACC
257 TAAAGATAGCAGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCAAAAACGGCAGATTTTACC
* *
23503 T-CATCGTGGTTACAGTGGAGTACATTGAAGCC-AGTAATTCTACTTC-CTTGGGCAGCAGCGGA
322 TCCCT-GTGGTTACAGTGAAGTACATTGAAGCCGA-TAATTCTACTTCTC-TGGGCAGCAGCGGA
* * * * * * *
23565 ATAGATTGACGATAGCAGATCTTGCCTTCCTACATAGACAGTGAAGCAGATCGAAGATGGCGGAT
384 ATAGATTAAAGATAGCAGATCTTGCATTCCTACATAGACAGCGAAGCAGATCAAAAATGGAGGAT
*
23630 TTTACCTCCTCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA
449 TTTACCTCATCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA
23678 TCTCCCTGGG
Statistics
Matches: 448, Mismatches: 41, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
505 6 0.01
506 440 0.98
507 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (506 bp):
AGATCTTGCCTTCCTACATAGACAACAAAGAAGATCGAAGATGGCAGATTTTACCTCCTCGTGGT
TACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAGAT
AGCAGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCGAAGACGGAGAATTTTACCTCCTCGT
GGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTAGGCAGCATCGGAATAGATTAAA
GATAGCAGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCAAAAACGGCAGATTTTACCTCCC
TGTGGTTACAGTGAAGTACATTGAAGCCGATAATTCTACTTCTCTGGGCAGCAGCGGAATAGATT
AAAGATAGCAGATCTTGCATTCCTACATAGACAGCGAAGCAGATCAAAAATGGAGGATTTTACCT
CATCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTAGC
Found at i:24537 original size:23 final size:22
Alignment explanation
Indices: 24492--24537 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
24482 TCACGCCAGT
* *
24492 TGCTCCCGCACGTCGCGCTTAC
1 TGCTCCCGCACGTCGCACGTAC
24514 TGCTCCGCGCACGTCGCACGTAC
1 TGCTCC-CGCACGTCGCACGTAC
24537 T
1 T
24538 CAACAGCCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.11, C:0.43, G:0.24, T:0.22
Consensus pattern (22 bp):
TGCTCCCGCACGTCGCACGTAC
Found at i:25484 original size:3 final size:3
Alignment explanation
Indices: 25476--25505 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
25466 TTTATCTTAC
*
25476 TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
25506 CTACTATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:27059 original size:22 final size:24
Alignment explanation
Indices: 27032--27095 Score: 82
Period size: 22 Copynumber: 2.8 Consensus size: 24
27022 TTATTTAAAA
27032 TAAATAAATTAATATTATTAAA-G
1 TAAATAAATTAATATTATTAAATG
27055 -AAATAAATTAA-ATTACTTAAATG
1 TAAATAAATTAATATTA-TTAAATG
*
27078 TTAATAAA-TAATATTATT
1 TAAATAAATTAATATTATT
27096 GAAAATGTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
21 4 0.11
22 16 0.44
23 6 0.17
24 10 0.28
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.41
Consensus pattern (24 bp):
TAAATAAATTAATATTATTAAATG
Found at i:28798 original size:30 final size:30
Alignment explanation
Indices: 28736--28798 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
28726 AGCCCTATAT
* * *
28736 AGTTCCAAGCCTGTTGAAGACAGTAAGCAA
1 AGTTACAAGCCTGTTGAAGACAGCAAGAAA
*
28766 AGTTACAAGCCTGTTGAAGACGGCAAGAAA
1 AGTTACAAGCCTGTTGAAGACAGCAAGAAA
28796 AGT
1 AGT
28799 GCGAGCCTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.19
Consensus pattern (30 bp):
AGTTACAAGCCTGTTGAAGACAGCAAGAAA
Found at i:28815 original size:16 final size:16
Alignment explanation
Indices: 28794--28824 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28784 GACGGCAAGA
28794 AAAGTGCGAGCCTGTC
1 AAAGTGCGAGCCTGTC
*
28810 AAAGTGTGAGCCTGT
1 AAAGTGCGAGCCTGT
28825 TGAATTGCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.23
Consensus pattern (16 bp):
AAAGTGCGAGCCTGTC
Found at i:67871 original size:29 final size:28
Alignment explanation
Indices: 67824--67884 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
67814 ATGGCCAACC
* *
67824 ATGTTGATATTATGTTTTTGTTAAAGTGT
1 ATGTTGATATGATGATTTTGTT-AAGTGT
* *
67853 ATGTTGTTATGATGATTTTGTTGAGTGT
1 ATGTTGATATGATGATTTTGTTAAGTGT
67881 ATGT
1 ATGT
67885 AGCTTGTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.21, C:0.00, G:0.25, T:0.54
Consensus pattern (28 bp):
ATGTTGATATGATGATTTTGTTAAGTGT
Done.